1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
5 ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
7 ;;; This file is part of GNU Guix.
9 ;;; GNU Guix is free software; you can redistribute it and/or modify it
10 ;;; under the terms of the GNU General Public License as published by
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12 ;;; your option) any later version.
14 ;;; GNU Guix is distributed in the hope that it will be useful, but
15 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
16 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 ;;; GNU General Public License for more details.
19 ;;; You should have received a copy of the GNU General Public License
20 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
22 (define-module (gnu packages bioconductor)
23 #:use-module ((guix licenses) #:prefix license:)
24 #:use-module (guix packages)
25 #:use-module (guix download)
26 #:use-module (guix git-download)
27 #:use-module (guix build-system r)
28 #:use-module (gnu packages)
29 #:use-module (gnu packages base)
30 #:use-module (gnu packages bioinformatics)
31 #:use-module (gnu packages cran)
32 #:use-module (gnu packages compression)
33 #:use-module (gnu packages gcc)
34 #:use-module (gnu packages graph)
35 #:use-module (gnu packages graphviz)
36 #:use-module (gnu packages haskell-xyz)
37 #:use-module (gnu packages image)
38 #:use-module (gnu packages maths)
39 #:use-module (gnu packages netpbm)
40 #:use-module (gnu packages perl)
41 #:use-module (gnu packages pkg-config)
42 #:use-module (gnu packages statistics)
43 #:use-module (gnu packages web)
44 #:use-module (gnu packages xml)
45 #:use-module (srfi srfi-1))
50 (define-public r-reactome-db
52 (name "r-reactome-db")
57 (uri (bioconductor-uri "reactome.db" version 'annotation))
60 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
61 (properties `((upstream-name . "reactome.db")))
62 (build-system r-build-system)
64 `(("r-annotationdbi" ,r-annotationdbi)))
65 (home-page "https://bioconductor.org/packages/reactome.db/")
66 (synopsis "Annotation maps for reactome")
68 "This package provides a set of annotation maps for the REACTOME
69 database, assembled using data from REACTOME.")
70 (license license:cc-by4.0)))
72 (define-public r-bsgenome-celegans-ucsc-ce6
74 (name "r-bsgenome-celegans-ucsc-ce6")
78 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
82 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
84 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
85 (build-system r-build-system)
87 `(("r-bsgenome" ,r-bsgenome)))
89 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
90 (synopsis "Full genome sequences for Worm")
92 "This package provides full genome sequences for Caenorhabditis
93 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
95 (license license:artistic2.0)))
97 (define-public r-bsgenome-celegans-ucsc-ce10
99 (name "r-bsgenome-celegans-ucsc-ce10")
103 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
104 version 'annotation))
107 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
109 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
110 (build-system r-build-system)
112 `(("r-bsgenome" ,r-bsgenome)))
114 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
115 (synopsis "Full genome sequences for Worm")
117 "This package provides full genome sequences for Caenorhabditis
118 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
120 (license license:artistic2.0)))
122 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
124 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
128 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
129 version 'annotation))
132 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
134 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
135 (build-system r-build-system)
137 `(("r-bsgenome" ,r-bsgenome)))
139 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
140 (synopsis "Full genome sequences for Fly")
142 "This package provides full genome sequences for Drosophila
143 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
145 (license license:artistic2.0)))
147 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
149 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
153 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
154 version 'annotation))
157 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
159 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
160 (build-system r-build-system)
162 `(("r-bsgenome" ,r-bsgenome)))
164 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
165 (synopsis "Full genome sequences for Fly")
167 "This package provides full genome sequences for Drosophila
168 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
169 Biostrings objects.")
170 (license license:artistic2.0)))
172 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
174 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
178 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
179 version 'annotation))
182 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
184 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
185 (build-system r-build-system)
187 `(("r-bsgenome" ,r-bsgenome)
188 ("r-bsgenome-dmelanogaster-ucsc-dm3"
189 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
190 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
191 (synopsis "Full masked genome sequences for Fly")
193 "This package provides full masked genome sequences for Drosophila
194 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
195 Biostrings objects. The sequences are the same as in
196 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
197 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
198 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
199 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
200 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
201 (license license:artistic2.0)))
203 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
205 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
209 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
210 version 'annotation))
213 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
215 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
216 (build-system r-build-system)
218 `(("r-bsgenome" ,r-bsgenome)))
220 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
221 (synopsis "Full genome sequences for Homo sapiens")
223 "This package provides full genome sequences for Homo sapiens from
224 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
225 (license license:artistic2.0)))
227 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
229 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
233 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
234 version 'annotation))
237 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
239 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
240 (build-system r-build-system)
242 `(("r-bsgenome" ,r-bsgenome)
243 ("r-bsgenome-hsapiens-ucsc-hg19"
244 ,r-bsgenome-hsapiens-ucsc-hg19)))
245 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
246 (synopsis "Full masked genome sequences for Homo sapiens")
248 "This package provides full genome sequences for Homo sapiens (Human) as
249 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
250 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
251 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
252 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
253 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
254 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
256 (license license:artistic2.0)))
258 (define-public r-bsgenome-mmusculus-ucsc-mm9
260 (name "r-bsgenome-mmusculus-ucsc-mm9")
264 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
265 version 'annotation))
268 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
270 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
271 (build-system r-build-system)
273 `(("r-bsgenome" ,r-bsgenome)))
275 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
276 (synopsis "Full genome sequences for Mouse")
278 "This package provides full genome sequences for Mus musculus (Mouse) as
279 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
280 (license license:artistic2.0)))
282 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
284 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
288 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
289 version 'annotation))
292 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
294 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
295 (build-system r-build-system)
297 `(("r-bsgenome" ,r-bsgenome)
298 ("r-bsgenome-mmusculus-ucsc-mm9"
299 ,r-bsgenome-mmusculus-ucsc-mm9)))
300 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
301 (synopsis "Full masked genome sequences for Mouse")
303 "This package provides full genome sequences for Mus musculus (Mouse) as
304 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
305 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
306 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
307 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
308 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
309 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
311 (license license:artistic2.0)))
313 (define-public r-bsgenome-mmusculus-ucsc-mm10
315 (name "r-bsgenome-mmusculus-ucsc-mm10")
319 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
320 version 'annotation))
323 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
325 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
326 (build-system r-build-system)
328 `(("r-bsgenome" ,r-bsgenome)))
330 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
331 (synopsis "Full genome sequences for Mouse")
333 "This package provides full genome sequences for Mus
334 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
335 in Biostrings objects.")
336 (license license:artistic2.0)))
338 (define-public r-org-ce-eg-db
340 (name "r-org-ce-eg-db")
344 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
347 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
349 `((upstream-name . "org.Ce.eg.db")))
350 (build-system r-build-system)
352 `(("r-annotationdbi" ,r-annotationdbi)))
353 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
354 (synopsis "Genome wide annotation for Worm")
356 "This package provides mappings from Entrez gene identifiers to various
357 annotations for the genome of the model worm Caenorhabditis elegans.")
358 (license license:artistic2.0)))
360 (define-public r-org-dm-eg-db
362 (name "r-org-dm-eg-db")
366 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
369 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
371 `((upstream-name . "org.Dm.eg.db")))
372 (build-system r-build-system)
374 `(("r-annotationdbi" ,r-annotationdbi)))
375 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
376 (synopsis "Genome wide annotation for Fly")
378 "This package provides mappings from Entrez gene identifiers to various
379 annotations for the genome of the model fruit fly Drosophila melanogaster.")
380 (license license:artistic2.0)))
382 (define-public r-org-dr-eg-db
384 (name "r-org-dr-eg-db")
388 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
391 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
393 `((upstream-name . "org.Dr.eg.db")))
394 (build-system r-build-system)
396 `(("r-annotationdbi" ,r-annotationdbi)))
397 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
398 (synopsis "Annotation for Zebrafish")
400 "This package provides genome wide annotations for Zebrafish, primarily
401 based on mapping using Entrez Gene identifiers.")
402 (license license:artistic2.0)))
404 (define-public r-org-hs-eg-db
406 (name "r-org-hs-eg-db")
410 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
413 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
415 `((upstream-name . "org.Hs.eg.db")))
416 (build-system r-build-system)
418 `(("r-annotationdbi" ,r-annotationdbi)))
419 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
420 (synopsis "Genome wide annotation for Human")
422 "This package contains genome-wide annotations for Human, primarily based
423 on mapping using Entrez Gene identifiers.")
424 (license license:artistic2.0)))
426 (define-public r-org-mm-eg-db
428 (name "r-org-mm-eg-db")
432 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
435 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
437 `((upstream-name . "org.Mm.eg.db")))
438 (build-system r-build-system)
440 `(("r-annotationdbi" ,r-annotationdbi)))
441 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
442 (synopsis "Genome wide annotation for Mouse")
444 "This package provides mappings from Entrez gene identifiers to various
445 annotations for the genome of the model mouse Mus musculus.")
446 (license license:artistic2.0)))
448 (define-public r-bsgenome-hsapiens-ucsc-hg19
450 (name "r-bsgenome-hsapiens-ucsc-hg19")
454 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
455 version 'annotation))
458 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
460 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
461 (build-system r-build-system)
463 `(("r-bsgenome" ,r-bsgenome)))
465 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
466 (synopsis "Full genome sequences for Homo sapiens")
468 "This package provides full genome sequences for Homo sapiens as provided
469 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
470 (license license:artistic2.0)))
472 (define-public r-ensdb-hsapiens-v75
474 (name "r-ensdb-hsapiens-v75")
479 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
482 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
484 `((upstream-name . "EnsDb.Hsapiens.v75")))
485 (build-system r-build-system)
487 `(("r-ensembldb" ,r-ensembldb)))
488 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
489 (synopsis "Ensembl based annotation package")
491 "This package exposes an annotation database generated from Ensembl.")
492 (license license:artistic2.0)))
494 (define-public r-genelendatabase
496 (name "r-genelendatabase")
501 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
504 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
506 `((upstream-name . "geneLenDataBase")))
507 (build-system r-build-system)
509 `(("r-rtracklayer" ,r-rtracklayer)
510 ("r-genomicfeatures" ,r-genomicfeatures)))
511 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
512 (synopsis "Lengths of mRNA transcripts for a number of genomes")
514 "This package provides the lengths of mRNA transcripts for a number of
515 genomes and gene ID formats, largely based on the UCSC table browser.")
516 (license license:lgpl2.0+)))
518 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
520 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
524 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
525 version 'annotation))
528 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
530 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
531 (build-system r-build-system)
533 `(("r-genomicfeatures" ,r-genomicfeatures)))
535 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
536 (synopsis "Annotation package for human genome in TxDb format")
538 "This package provides an annotation database of Homo sapiens genome
539 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
540 track. The database is exposed as a @code{TxDb} object.")
541 (license license:artistic2.0)))
543 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
545 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
549 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
550 version 'annotation))
553 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
555 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
556 (build-system r-build-system)
558 `(("r-genomicfeatures" ,r-genomicfeatures)))
560 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
561 (synopsis "Annotation package for human genome in TxDb format")
563 "This package provides an annotation database of Homo sapiens genome
564 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
565 track. The database is exposed as a @code{TxDb} object.")
566 (license license:artistic2.0)))
568 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
570 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
574 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
575 version 'annotation))
578 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
580 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
581 (build-system r-build-system)
583 `(("r-genomicfeatures" ,r-genomicfeatures)
584 ("r-annotationdbi" ,r-annotationdbi)))
586 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
587 (synopsis "Annotation package for mouse genome in TxDb format")
589 "This package provides an annotation database of Mouse genome data. It
590 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
591 database is exposed as a @code{TxDb} object.")
592 (license license:artistic2.0)))
594 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
596 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
600 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
601 version 'annotation))
604 "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
606 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
607 (build-system r-build-system)
609 `(("r-bsgenome" ,r-bsgenome)
610 ("r-genomicfeatures" ,r-genomicfeatures)
611 ("r-annotationdbi" ,r-annotationdbi)))
613 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
614 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
616 "This package loads a TxDb object, which is an R interface to
617 prefabricated databases contained in this package. This package provides
618 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
619 based on the knownGene track.")
620 (license license:artistic2.0)))
622 (define-public r-txdb-celegans-ucsc-ce6-ensgene
624 (name "r-txdb-celegans-ucsc-ce6-ensgene")
629 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
630 version 'annotation))
633 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
635 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
636 (build-system r-build-system)
638 `(("r-annotationdbi" ,r-annotationdbi)
639 ("r-genomicfeatures" ,r-genomicfeatures)))
640 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
641 (synopsis "Annotation package for C elegans TxDb objects")
643 "This package exposes a C elegans annotation database generated from UCSC
644 by exposing these as TxDb objects.")
645 (license license:artistic2.0)))
647 (define-public r-fdb-infiniummethylation-hg19
649 (name "r-fdb-infiniummethylation-hg19")
653 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
654 version 'annotation))
657 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
659 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
660 (build-system r-build-system)
662 `(("r-biostrings" ,r-biostrings)
663 ("r-genomicfeatures" ,r-genomicfeatures)
664 ("r-annotationdbi" ,r-annotationdbi)
665 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
666 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
667 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
668 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
670 "This is an annotation package for Illumina Infinium DNA methylation
671 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
673 (license license:artistic2.0)))
675 (define-public r-illuminahumanmethylationepicmanifest
677 (name "r-illuminahumanmethylationepicmanifest")
681 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
682 version 'annotation))
685 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
687 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
688 (build-system r-build-system)
690 `(("r-minfi" ,r-minfi)))
691 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
692 (synopsis "Manifest for Illumina's EPIC methylation arrays")
694 "This is a manifest package for Illumina's EPIC methylation arrays.")
695 (license license:artistic2.0)))
697 (define-public r-do-db
703 (uri (bioconductor-uri "DO.db" version 'annotation))
706 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
708 `((upstream-name . "DO.db")))
709 (build-system r-build-system)
711 `(("r-annotationdbi" ,r-annotationdbi)))
712 (home-page "https://www.bioconductor.org/packages/DO.db/")
713 (synopsis "Annotation maps describing the entire Disease Ontology")
715 "This package provides a set of annotation maps describing the entire
717 (license license:artistic2.0)))
719 (define-public r-pfam-db
726 (uri (bioconductor-uri "PFAM.db" version 'annotation))
729 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
730 (properties `((upstream-name . "PFAM.db")))
731 (build-system r-build-system)
733 `(("r-annotationdbi" ,r-annotationdbi)))
734 (home-page "https://bioconductor.org/packages/PFAM.db")
735 (synopsis "Set of protein ID mappings for PFAM")
737 "This package provides a set of protein ID mappings for PFAM, assembled
738 using data from public repositories.")
739 (license license:artistic2.0)))
741 (define-public r-phastcons100way-ucsc-hg19
743 (name "r-phastcons100way-ucsc-hg19")
748 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
749 version 'annotation))
752 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
754 `((upstream-name . "phastCons100way.UCSC.hg19")))
755 (build-system r-build-system)
757 `(("r-bsgenome" ,r-bsgenome)
758 ("r-genomeinfodb" ,r-genomeinfodb)
759 ("r-genomicranges" ,r-genomicranges)
760 ("r-genomicscores" ,r-genomicscores)
761 ("r-iranges" ,r-iranges)
762 ("r-s4vectors" ,r-s4vectors)))
763 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
764 (synopsis "UCSC phastCons conservation scores for hg19")
766 "This package provides UCSC phastCons conservation scores for the human
767 genome (hg19) calculated from multiple alignments with other 99 vertebrate
769 (license license:artistic2.0)))
774 (define-public r-abadata
780 (uri (bioconductor-uri "ABAData" version 'experiment))
783 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
785 `((upstream-name . "ABAData")))
786 (build-system r-build-system)
788 `(("r-annotationdbi" ,r-annotationdbi)))
789 (home-page "https://www.bioconductor.org/packages/ABAData/")
790 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
792 "This package provides the data for the gene expression enrichment
793 analysis conducted in the package ABAEnrichment. The package includes three
794 datasets which are derived from the Allen Brain Atlas:
797 @item Gene expression data from Human Brain (adults) averaged across donors,
798 @item Gene expression data from the Developing Human Brain pooled into five
799 age categories and averaged across donors, and
800 @item a developmental effect score based on the Developing Human Brain
804 All datasets are restricted to protein coding genes.")
805 (license license:gpl2+)))
807 (define-public r-arrmdata
813 (uri (bioconductor-uri "ARRmData" version 'experiment))
816 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
818 `((upstream-name . "ARRmData")))
819 (build-system r-build-system)
820 (home-page "https://www.bioconductor.org/packages/ARRmData/")
821 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
823 "This package provides raw beta values from 36 samples across 3 groups
824 from Illumina 450k methylation arrays.")
825 (license license:artistic2.0)))
827 (define-public r-hsmmsinglecell
829 (name "r-hsmmsinglecell")
833 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
836 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
838 `((upstream-name . "HSMMSingleCell")))
839 (build-system r-build-system)
840 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
841 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
843 "Skeletal myoblasts undergo a well-characterized sequence of
844 morphological and transcriptional changes during differentiation. In this
845 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
846 under high mitogen conditions (GM) and then differentiated by switching to
847 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
848 hundred cells taken over a time-course of serum-induced differentiation.
849 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
850 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
851 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
852 which were then sequenced to a depth of ~4 million reads per library,
853 resulting in a complete gene expression profile for each cell.")
854 (license license:artistic2.0)))
862 (uri (bioconductor-uri "ALL" version 'experiment))
865 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
866 (properties `((upstream-name . "ALL")))
867 (build-system r-build-system)
869 `(("r-biobase" ,r-biobase)))
870 (home-page "https://bioconductor.org/packages/ALL")
871 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
873 "The data consist of microarrays from 128 different individuals with
874 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
875 are available. The data have been normalized (using rma) and it is the
876 jointly normalized data that are available here. The data are presented in
877 the form of an @code{exprSet} object.")
878 (license license:artistic2.0)))
880 (define-public r-affydata
887 (uri (bioconductor-uri "affydata" version 'experiment))
890 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
891 (properties `((upstream-name . "affydata")))
892 (build-system r-build-system)
894 `(("r-affy" ,r-affy)))
895 (home-page "https://bioconductor.org/packages/affydata/")
896 (synopsis "Affymetrix data for demonstration purposes")
898 "This package provides example datasets that represent 'real world
899 examples' of Affymetrix data, unlike the artificial examples included in the
900 package @code{affy}.")
901 (license license:gpl2+)))
903 (define-public r-curatedtcgadata
905 (name "r-curatedtcgadata")
910 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
913 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
915 `((upstream-name . "curatedTCGAData")))
916 (build-system r-build-system)
918 `(("r-annotationhub" ,r-annotationhub)
919 ("r-experimenthub" ,r-experimenthub)
920 ("r-hdf5array" ,r-hdf5array)
921 ("r-multiassayexperiment" ,r-multiassayexperiment)
922 ("r-s4vectors" ,r-s4vectors)
923 ("r-summarizedexperiment" ,r-summarizedexperiment)))
924 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
925 (synopsis "Curated data from The Cancer Genome Atlas")
927 "This package provides publicly available data from The Cancer Genome
928 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
929 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
930 number, mutation, microRNA, protein, and others) with clinical / pathological
931 data. It also links assay barcodes with patient identifiers, enabling
932 harmonized subsetting of rows (features) and columns (patients / samples)
933 across the entire multi-'omics experiment.")
934 (license license:artistic2.0)))
939 (define-public r-biocversion
941 (name "r-biocversion")
946 (uri (bioconductor-uri "BiocVersion" version))
949 "0mfqjqfvrwwglldq3g7nbic5hf3nwzv02nbfxnl2cfvf9gznlh5f"))))
950 (properties `((upstream-name . "BiocVersion")))
951 (build-system r-build-system)
952 (home-page "https://bioconductor.org/packages/BiocVersion/")
953 (synopsis "Set the appropriate version of Bioconductor packages")
955 "This package provides repository information for the appropriate version
957 (license license:artistic2.0)))
959 (define-public r-biocgenerics
961 (name "r-biocgenerics")
965 (uri (bioconductor-uri "BiocGenerics" version))
968 "1np8y442zyakm4axpinbw1qsgc6wd3zjsnirbhc8lcii4ky9j0rn"))))
970 `((upstream-name . "BiocGenerics")))
971 (build-system r-build-system)
972 (home-page "https://bioconductor.org/packages/BiocGenerics")
973 (synopsis "S4 generic functions for Bioconductor")
975 "This package provides S4 generic functions needed by many Bioconductor
977 (license license:artistic2.0)))
979 (define-public r-affycomp
986 (uri (bioconductor-uri "affycomp" version))
989 "0cl7c3m2lz2w8g2k7z7wjd0dyj0dkssvms99qpg8a1v3hx1xs6js"))))
990 (properties `((upstream-name . "affycomp")))
991 (build-system r-build-system)
992 (propagated-inputs `(("r-biobase" ,r-biobase)))
993 (home-page "https://bioconductor.org/packages/affycomp/")
994 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
996 "The package contains functions that can be used to compare expression
997 measures for Affymetrix Oligonucleotide Arrays.")
998 (license license:gpl2+)))
1000 (define-public r-affycompatible
1002 (name "r-affycompatible")
1007 (uri (bioconductor-uri "AffyCompatible" version))
1010 "10ahrdlifp1i7rd58zb10w75y5bnigs7xp5gv4fhb5y7p7dvb0ks"))))
1012 `((upstream-name . "AffyCompatible")))
1013 (build-system r-build-system)
1015 `(("r-biostrings" ,r-biostrings)
1016 ("r-rcurl" ,r-rcurl)
1018 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1019 (synopsis "Work with Affymetrix GeneChip files")
1021 "This package provides an interface to Affymetrix chip annotation and
1022 sample attribute files. The package allows an easy way for users to download
1023 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1024 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1025 Command Console} (AGCC)-compatible sample annotation files.")
1026 (license license:artistic2.0)))
1028 (define-public r-affycontam
1030 (name "r-affycontam")
1035 (uri (bioconductor-uri "affyContam" version))
1038 "0yd1prgv5zfkg22ski73mvg96qknwz8v6ji6s4qy8p4wrqyj7b7l"))))
1039 (properties `((upstream-name . "affyContam")))
1040 (build-system r-build-system)
1042 `(("r-affy" ,r-affy)
1043 ("r-affydata" ,r-affydata)
1044 ("r-biobase" ,r-biobase)))
1045 (home-page "https://bioconductor.org/packages/affyContam/")
1046 (synopsis "Structured corruption of Affymetrix CEL file data")
1048 "Microarray quality assessment is a major concern of microarray analysts.
1049 This package provides some simple approaches to in silico creation of quality
1050 problems in CEL-level data to help evaluate performance of quality metrics.")
1051 (license license:artistic2.0)))
1053 (define-public r-affycoretools
1055 (name "r-affycoretools")
1060 (uri (bioconductor-uri "affycoretools" version))
1063 "1p283ysib04qzaayxmrpsmk5bq0jdq2rlky180jrlskpyg6risfw"))))
1064 (properties `((upstream-name . "affycoretools")))
1065 (build-system r-build-system)
1067 `(("r-affy" ,r-affy)
1068 ("r-annotationdbi" ,r-annotationdbi)
1069 ("r-biobase" ,r-biobase)
1070 ("r-biocgenerics" ,r-biocgenerics)
1072 ("r-edger" ,r-edger)
1073 ("r-gcrma" ,r-gcrma)
1074 ("r-glimma" ,r-glimma)
1075 ("r-ggplot2" ,r-ggplot2)
1076 ("r-gostats" ,r-gostats)
1077 ("r-gplots" ,r-gplots)
1078 ("r-hwriter" ,r-hwriter)
1079 ("r-lattice" ,r-lattice)
1080 ("r-limma" ,r-limma)
1081 ("r-oligoclasses" ,r-oligoclasses)
1082 ("r-reportingtools" ,r-reportingtools)
1083 ("r-rsqlite" ,r-rsqlite)
1084 ("r-s4vectors" ,r-s4vectors)
1085 ("r-xtable" ,r-xtable)))
1086 (home-page "https://bioconductor.org/packages/affycoretools/")
1087 (synopsis "Functions for analyses with Affymetrix GeneChips")
1089 "This package provides various wrapper functions that have been written
1090 to streamline the more common analyses that a Biostatistician might see.")
1091 (license license:artistic2.0)))
1093 (define-public r-affxparser
1095 (name "r-affxparser")
1100 (uri (bioconductor-uri "affxparser" version))
1103 "03h4lxr48p84f6i7zb2rm10ma3k4d1nmvdw5yhxcmzqbmd12lk40"))))
1104 (properties `((upstream-name . "affxparser")))
1105 (build-system r-build-system)
1106 (home-page "https://github.com/HenrikBengtsson/affxparser")
1107 (synopsis "Affymetrix File Parsing SDK")
1109 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1110 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1111 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1112 are supported. Currently, there are methods for reading @dfn{chip definition
1113 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1114 either in full or in part. For example, probe signals from a few probesets
1115 can be extracted very quickly from a set of CEL files into a convenient list
1117 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1119 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1121 (define-public r-annotate
1128 (uri (bioconductor-uri "annotate" version))
1131 "0rcmdy6hs6m4d6wxgi52c0bhdsbf2sm9f155qbcb05sn0nh8pxwy"))))
1132 (build-system r-build-system)
1134 `(("r-annotationdbi" ,r-annotationdbi)
1135 ("r-biobase" ,r-biobase)
1136 ("r-biocgenerics" ,r-biocgenerics)
1138 ("r-rcurl" ,r-rcurl)
1140 ("r-xtable" ,r-xtable)))
1142 "https://bioconductor.org/packages/annotate")
1143 (synopsis "Annotation for microarrays")
1144 (description "This package provides R environments for the annotation of
1146 (license license:artistic2.0)))
1148 (define-public r-hpar
1155 (uri (bioconductor-uri "hpar" version))
1158 "1yhay1ryrgj9cqa1x136cw40ca93afyvg0sarm30jsbj8nc1rm5m"))))
1159 (build-system r-build-system)
1160 (home-page "https://bioconductor.org/packages/hpar/")
1161 (synopsis "Human Protein Atlas in R")
1162 (description "This package provides a simple interface to and data from
1163 the Human Protein Atlas project.")
1164 (license license:artistic2.0)))
1166 (define-public r-regioner
1173 (uri (bioconductor-uri "regioneR" version))
1176 "0if7r6njz3ahm545383z5mzmzw8fdvw80a9lfz160j5pcgpx2dq9"))))
1177 (properties `((upstream-name . "regioneR")))
1178 (build-system r-build-system)
1180 `(("r-biostrings" ,r-biostrings)
1181 ("r-bsgenome" ,r-bsgenome)
1182 ("r-genomeinfodb" ,r-genomeinfodb)
1183 ("r-genomicranges" ,r-genomicranges)
1184 ("r-iranges" ,r-iranges)
1185 ("r-memoise" ,r-memoise)
1186 ("r-rtracklayer" ,r-rtracklayer)
1187 ("r-s4vectors" ,r-s4vectors)))
1188 (home-page "https://bioconductor.org/packages/regioneR/")
1189 (synopsis "Association analysis of genomic regions")
1190 (description "This package offers a statistical framework based on
1191 customizable permutation tests to assess the association between genomic
1192 region sets and other genomic features.")
1193 (license license:artistic2.0)))
1195 (define-public r-reportingtools
1197 (name "r-reportingtools")
1202 (uri (bioconductor-uri "ReportingTools" version))
1205 "0wmi2219wydyzc07rz3azsrksa7wiacfh9pr5x2fsmj9f0w3n15w"))))
1207 `((upstream-name . "ReportingTools")))
1208 (build-system r-build-system)
1210 `(("r-annotate" ,r-annotate)
1211 ("r-annotationdbi" ,r-annotationdbi)
1212 ("r-biobase" ,r-biobase)
1213 ("r-biocgenerics" ,r-biocgenerics)
1214 ("r-category" ,r-category)
1215 ("r-deseq2" ,r-deseq2)
1216 ("r-edger" ,r-edger)
1217 ("r-ggbio" ,r-ggbio)
1218 ("r-ggplot2" ,r-ggplot2)
1219 ("r-gostats" ,r-gostats)
1220 ("r-gseabase" ,r-gseabase)
1221 ("r-hwriter" ,r-hwriter)
1222 ("r-iranges" ,r-iranges)
1223 ("r-knitr" ,r-knitr)
1224 ("r-lattice" ,r-lattice)
1225 ("r-limma" ,r-limma)
1226 ("r-pfam-db" ,r-pfam-db)
1227 ("r-r-utils" ,r-r-utils)
1229 (home-page "https://bioconductor.org/packages/ReportingTools/")
1230 (synopsis "Tools for making reports in various formats")
1232 "The ReportingTools package enables users to easily display reports of
1233 analysis results generated from sources such as microarray and sequencing
1234 data. The package allows users to create HTML pages that may be viewed on a
1235 web browser, or in other formats. Users can generate tables with sortable and
1236 filterable columns, make and display plots, and link table entries to other
1237 data sources such as NCBI or larger plots within the HTML page. Using the
1238 package, users can also produce a table of contents page to link various
1239 reports together for a particular project that can be viewed in a web
1241 (license license:artistic2.0)))
1243 (define-public r-geneplotter
1245 (name "r-geneplotter")
1250 (uri (bioconductor-uri "geneplotter" version))
1253 "1k6780fn1kkghpm1prhhsyw621441a3bmnqfl9ns0zbc1zdq39nx"))))
1254 (build-system r-build-system)
1256 `(("r-annotate" ,r-annotate)
1257 ("r-annotationdbi" ,r-annotationdbi)
1258 ("r-biobase" ,r-biobase)
1259 ("r-biocgenerics" ,r-biocgenerics)
1260 ("r-lattice" ,r-lattice)
1261 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1262 (home-page "https://bioconductor.org/packages/geneplotter")
1263 (synopsis "Graphics functions for genomic data")
1265 "This package provides functions for plotting genomic data.")
1266 (license license:artistic2.0)))
1268 (define-public r-oligoclasses
1270 (name "r-oligoclasses")
1275 (uri (bioconductor-uri "oligoClasses" version))
1278 "02m1m3dkiyywalphw3i5n6y3bs8zp24xh59v9cz6jgjpah811skf"))))
1279 (properties `((upstream-name . "oligoClasses")))
1280 (build-system r-build-system)
1282 `(("r-affyio" ,r-affyio)
1283 ("r-biobase" ,r-biobase)
1284 ("r-biocgenerics" ,r-biocgenerics)
1285 ("r-biocmanager" ,r-biocmanager)
1286 ("r-biostrings" ,r-biostrings)
1289 ("r-foreach" ,r-foreach)
1290 ("r-genomicranges" ,r-genomicranges)
1291 ("r-iranges" ,r-iranges)
1292 ("r-rsqlite" ,r-rsqlite)
1293 ("r-s4vectors" ,r-s4vectors)
1294 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1295 (home-page "https://bioconductor.org/packages/oligoClasses/")
1296 (synopsis "Classes for high-throughput arrays")
1298 "This package contains class definitions, validity checks, and
1299 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1301 (license license:gpl2+)))
1303 (define-public r-oligo
1310 (uri (bioconductor-uri "oligo" version))
1313 "01icfyy82f9k0m7ngrppz1ckq3wpq7zp6kgf8ppc55j6582c5jh3"))))
1314 (properties `((upstream-name . "oligo")))
1315 (build-system r-build-system)
1316 (inputs `(("zlib" ,zlib)))
1318 `(("r-affxparser" ,r-affxparser)
1319 ("r-affyio" ,r-affyio)
1320 ("r-biobase" ,r-biobase)
1321 ("r-biocgenerics" ,r-biocgenerics)
1322 ("r-biostrings" ,r-biostrings)
1325 ("r-oligoclasses" ,r-oligoclasses)
1326 ("r-preprocesscore" ,r-preprocesscore)
1327 ("r-rsqlite" ,r-rsqlite)
1328 ("r-zlibbioc" ,r-zlibbioc)))
1329 (home-page "https://bioconductor.org/packages/oligo/")
1330 (synopsis "Preprocessing tools for oligonucleotide arrays")
1332 "This package provides a package to analyze oligonucleotide
1333 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1334 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1335 (license license:lgpl2.0+)))
1337 (define-public r-qvalue
1344 (uri (bioconductor-uri "qvalue" version))
1347 "0njnidyncm3g3712mnp77cs4kghn596ss1pz6fhp1cr0wxcayp6j"))))
1348 (build-system r-build-system)
1350 `(("r-ggplot2" ,r-ggplot2)
1351 ("r-reshape2" ,r-reshape2)))
1352 (home-page "http://github.com/jdstorey/qvalue")
1353 (synopsis "Q-value estimation for false discovery rate control")
1355 "This package takes a list of p-values resulting from the simultaneous
1356 testing of many hypotheses and estimates their q-values and local @dfn{false
1357 discovery rate} (FDR) values. The q-value of a test measures the proportion
1358 of false positives incurred when that particular test is called significant.
1359 The local FDR measures the posterior probability the null hypothesis is true
1360 given the test's p-value. Various plots are automatically generated, allowing
1361 one to make sensible significance cut-offs. The software can be applied to
1362 problems in genomics, brain imaging, astrophysics, and data mining.")
1363 ;; Any version of the LGPL.
1364 (license license:lgpl3+)))
1366 (define-public r-diffbind
1373 (uri (bioconductor-uri "DiffBind" version))
1376 "1729wyi2l4480yrkp5wg3ryirrmlk0j3njqs1qyckq3c8bjk12h2"))))
1377 (properties `((upstream-name . "DiffBind")))
1378 (build-system r-build-system)
1382 `(("r-amap" ,r-amap)
1383 ("r-biocparallel" ,r-biocparallel)
1384 ("r-deseq2" ,r-deseq2)
1385 ("r-dplyr" ,r-dplyr)
1386 ("r-edger" ,r-edger)
1387 ("r-genomicalignments" ,r-genomicalignments)
1388 ("r-genomicranges" ,r-genomicranges)
1389 ("r-ggplot2" ,r-ggplot2)
1390 ("r-ggrepel" ,r-ggrepel)
1391 ("r-gplots" ,r-gplots)
1392 ("r-iranges" ,r-iranges)
1393 ("r-lattice" ,r-lattice)
1394 ("r-limma" ,r-limma)
1395 ("r-locfit" ,r-locfit)
1396 ("r-rcolorbrewer" , r-rcolorbrewer)
1398 ("r-rhtslib" ,r-rhtslib)
1399 ("r-rsamtools" ,r-rsamtools)
1400 ("r-s4vectors" ,r-s4vectors)
1401 ("r-summarizedexperiment" ,r-summarizedexperiment)
1402 ("r-systempiper" ,r-systempiper)))
1403 (home-page "http://bioconductor.org/packages/DiffBind")
1404 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1406 "This package computes differentially bound sites from multiple
1407 ChIP-seq experiments using affinity (quantitative) data. Also enables
1408 occupancy (overlap) analysis and plotting functions.")
1409 (license license:artistic2.0)))
1411 (define-public r-ripseeker
1413 (name "r-ripseeker")
1418 (uri (bioconductor-uri "RIPSeeker" version))
1421 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
1422 (properties `((upstream-name . "RIPSeeker")))
1423 (build-system r-build-system)
1425 `(("r-s4vectors" ,r-s4vectors)
1426 ("r-iranges" ,r-iranges)
1427 ("r-genomicranges" ,r-genomicranges)
1428 ("r-summarizedexperiment" ,r-summarizedexperiment)
1429 ("r-rsamtools" ,r-rsamtools)
1430 ("r-genomicalignments" ,r-genomicalignments)
1431 ("r-rtracklayer" ,r-rtracklayer)))
1432 (home-page "http://bioconductor.org/packages/RIPSeeker")
1434 "Identifying protein-associated transcripts from RIP-seq experiments")
1436 "This package infers and discriminates RIP peaks from RIP-seq alignments
1437 using two-state HMM with negative binomial emission probability. While
1438 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1439 a suite of bioinformatics tools integrated within this self-contained software
1440 package comprehensively addressing issues ranging from post-alignments
1441 processing to visualization and annotation.")
1442 (license license:gpl2)))
1444 (define-public r-multtest
1451 (uri (bioconductor-uri "multtest" version))
1454 "0qna9lx76ldsfy8qf5xmhl4ymqfkj29m1gdqhph06s470c8mwari"))))
1455 (build-system r-build-system)
1457 `(("r-survival" ,r-survival)
1458 ("r-biocgenerics" ,r-biocgenerics)
1459 ("r-biobase" ,r-biobase)
1460 ("r-mass" ,r-mass)))
1461 (home-page "http://bioconductor.org/packages/multtest")
1462 (synopsis "Resampling-based multiple hypothesis testing")
1464 "This package can do non-parametric bootstrap and permutation
1465 resampling-based multiple testing procedures (including empirical Bayes
1466 methods) for controlling the family-wise error rate (FWER), generalized
1467 family-wise error rate (gFWER), tail probability of the proportion of
1468 false positives (TPPFP), and false discovery rate (FDR). Several choices
1469 of bootstrap-based null distribution are implemented (centered, centered
1470 and scaled, quantile-transformed). Single-step and step-wise methods are
1471 available. Tests based on a variety of T- and F-statistics (including
1472 T-statistics based on regression parameters from linear and survival models
1473 as well as those based on correlation parameters) are included. When probing
1474 hypotheses with T-statistics, users may also select a potentially faster null
1475 distribution which is multivariate normal with mean zero and variance
1476 covariance matrix derived from the vector influence function. Results are
1477 reported in terms of adjusted P-values, confidence regions and test statistic
1478 cutoffs. The procedures are directly applicable to identifying differentially
1479 expressed genes in DNA microarray experiments.")
1480 (license license:lgpl3)))
1482 (define-public r-graph
1488 (uri (bioconductor-uri "graph" version))
1491 "1ivf59k7k552m7zd8g3wwazd71dq3xmgmhcq435738i02h0fqnyc"))))
1492 (build-system r-build-system)
1494 `(("r-biocgenerics" ,r-biocgenerics)))
1495 (home-page "https://bioconductor.org/packages/graph")
1496 (synopsis "Handle graph data structures in R")
1498 "This package implements some simple graph handling capabilities for R.")
1499 (license license:artistic2.0)))
1501 (define-public r-codedepends
1503 (name "r-codedepends")
1508 (uri (cran-uri "CodeDepends" version))
1511 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1512 (properties `((upstream-name . "CodeDepends")))
1513 (build-system r-build-system)
1515 `(("r-codetools" ,r-codetools)
1516 ("r-graph" ,r-graph)
1518 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1519 (synopsis "Analysis of R code for reproducible research and code comprehension")
1521 "This package provides tools for analyzing R expressions or blocks of
1522 code and determining the dependencies between them. It focuses on R scripts,
1523 but can be used on the bodies of functions. There are many facilities
1524 including the ability to summarize or get a high-level view of code,
1525 determining dependencies between variables, code improvement suggestions.")
1526 ;; Any version of the GPL
1527 (license (list license:gpl2+ license:gpl3+))))
1529 (define-public r-chippeakanno
1531 (name "r-chippeakanno")
1536 (uri (bioconductor-uri "ChIPpeakAnno" version))
1539 "0hp3s3shnrb55cxvx9wrdl67wqw9f55gdgx7262s4mahpxjswfsa"))))
1540 (properties `((upstream-name . "ChIPpeakAnno")))
1541 (build-system r-build-system)
1543 `(("r-annotationdbi" ,r-annotationdbi)
1544 ("r-biobase" ,r-biobase)
1545 ("r-biocgenerics" ,r-biocgenerics)
1546 ("r-biocmanager" ,r-biocmanager)
1547 ("r-biomart" ,r-biomart)
1548 ("r-biostrings" ,r-biostrings)
1549 ("r-bsgenome" ,r-bsgenome)
1551 ("r-delayedarray" ,r-delayedarray)
1552 ("r-ensembldb" ,r-ensembldb)
1553 ("r-genomeinfodb" ,r-genomeinfodb)
1554 ("r-genomicalignments" ,r-genomicalignments)
1555 ("r-genomicfeatures" ,r-genomicfeatures)
1556 ("r-genomicranges" ,r-genomicranges)
1557 ("r-go-db" ,r-go-db)
1558 ("r-graph" ,r-graph)
1560 ("r-iranges" ,r-iranges)
1561 ("r-limma" ,r-limma)
1562 ("r-matrixstats" ,r-matrixstats)
1563 ("r-multtest" ,r-multtest)
1565 ("r-regioner" ,r-regioner)
1566 ("r-rsamtools" ,r-rsamtools)
1567 ("r-rtracklayer" ,r-rtracklayer)
1568 ("r-s4vectors" ,r-s4vectors)
1569 ("r-seqinr" ,r-seqinr)
1570 ("r-summarizedexperiment" ,r-summarizedexperiment)
1571 ("r-venndiagram" ,r-venndiagram)))
1572 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1573 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1575 "The package includes functions to retrieve the sequences around the peak,
1576 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1577 custom features such as most conserved elements and other transcription factor
1578 binding sites supplied by users. Starting 2.0.5, new functions have been added
1579 for finding the peaks with bi-directional promoters with summary statistics
1580 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1581 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1582 enrichedGO (addGeneIDs).")
1583 (license license:gpl2+)))
1585 (define-public r-marray
1591 (uri (bioconductor-uri "marray" version))
1593 (base32 "1mbs9rk279hnm9yz34za3xz3hb88ll1d0abw4m2pgjgbh4kkhdrl"))))
1594 (build-system r-build-system)
1596 `(("r-limma" ,r-limma)))
1597 (home-page "http://bioconductor.org/packages/marray")
1598 (synopsis "Exploratory analysis for two-color spotted microarray data")
1599 (description "This package contains class definitions for two-color spotted
1600 microarray data. It also includes functions for data input, diagnostic plots,
1601 normalization and quality checking.")
1602 (license license:lgpl2.0+)))
1604 (define-public r-cghbase
1610 (uri (bioconductor-uri "CGHbase" version))
1612 (base32 "0136pk6pfwpiiy9vca4pgg4wh74jfb5ssglpdszzhamljpvg765x"))))
1613 (properties `((upstream-name . "CGHbase")))
1614 (build-system r-build-system)
1616 `(("r-biobase" ,r-biobase)
1617 ("r-marray" ,r-marray)))
1618 (home-page "http://bioconductor.org/packages/CGHbase")
1619 (synopsis "Base functions and classes for arrayCGH data analysis")
1620 (description "This package contains functions and classes that are needed by
1621 the @code{arrayCGH} packages.")
1622 (license license:gpl2+)))
1624 (define-public r-cghcall
1630 (uri (bioconductor-uri "CGHcall" version))
1632 (base32 "1x8pz7zhw2nabik1vgdhlivndqvil3s7vnl5070k493v6gza0p3s"))))
1633 (properties `((upstream-name . "CGHcall")))
1634 (build-system r-build-system)
1636 `(("r-biobase" ,r-biobase)
1637 ("r-cghbase" ,r-cghbase)
1638 ("r-impute" ,r-impute)
1639 ("r-dnacopy" ,r-dnacopy)
1640 ("r-snowfall" ,r-snowfall)))
1641 (home-page "http://bioconductor.org/packages/CGHcall")
1642 (synopsis "Base functions and classes for arrayCGH data analysis")
1643 (description "This package contains functions and classes that are needed by
1644 @code{arrayCGH} packages.")
1645 (license license:gpl2+)))
1647 (define-public r-qdnaseq
1653 (uri (bioconductor-uri "QDNAseq" version))
1655 (base32 "0xcqdpv9a47zpxx0q9sif5y4s1yzx3pig0kywy961kh5xgl5bcrq"))))
1656 (properties `((upstream-name . "QDNAseq")))
1657 (build-system r-build-system)
1659 `(("r-biobase" ,r-biobase)
1660 ("r-cghbase" ,r-cghbase)
1661 ("r-cghcall" ,r-cghcall)
1662 ("r-dnacopy" ,r-dnacopy)
1663 ("r-future" ,r-future)
1664 ("r-future-apply" ,r-future-apply)
1665 ("r-genomicranges" ,r-genomicranges)
1666 ("r-iranges" ,r-iranges)
1667 ("r-matrixstats" ,r-matrixstats)
1668 ("r-r-utils" ,r-r-utils)
1669 ("r-rsamtools" ,r-rsamtools)))
1670 (home-page "http://bioconductor.org/packages/QDNAseq")
1671 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1672 (description "The genome is divided into non-overlapping fixed-sized bins,
1673 number of sequence reads in each counted, adjusted with a simultaneous
1674 two-dimensional loess correction for sequence mappability and GC content, and
1675 filtered to remove spurious regions in the genome. Downstream steps of
1676 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1678 (license license:gpl2+)))
1680 (define-public r-bayseq
1687 (uri (bioconductor-uri "baySeq" version))
1690 "040s1d3756spyzblkyx2vcy7bn3vf87mhsp3is35yxkj55n3myjk"))))
1691 (properties `((upstream-name . "baySeq")))
1692 (build-system r-build-system)
1694 `(("r-abind" ,r-abind)
1695 ("r-edger" ,r-edger)
1696 ("r-genomicranges" ,r-genomicranges)))
1697 (home-page "https://bioconductor.org/packages/baySeq/")
1698 (synopsis "Bayesian analysis of differential expression patterns in count data")
1700 "This package identifies differential expression in high-throughput count
1701 data, such as that derived from next-generation sequencing machines,
1702 calculating estimated posterior likelihoods of differential expression (or
1703 more complex hypotheses) via empirical Bayesian methods.")
1704 (license license:gpl3)))
1706 (define-public r-chipcomp
1713 (uri (bioconductor-uri "ChIPComp" version))
1716 "0wk0vvg6dk9wk60lzbadrnqar75dppvyr4hiwrhv9rhhah2mg2mg"))))
1717 (properties `((upstream-name . "ChIPComp")))
1718 (build-system r-build-system)
1720 `(("r-biocgenerics" ,r-biocgenerics)
1721 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1722 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1723 ("r-genomeinfodb" ,r-genomeinfodb)
1724 ("r-genomicranges" ,r-genomicranges)
1725 ("r-iranges" ,r-iranges)
1726 ("r-limma" ,r-limma)
1727 ("r-rsamtools" ,r-rsamtools)
1728 ("r-rtracklayer" ,r-rtracklayer)
1729 ("r-s4vectors" ,r-s4vectors)))
1730 (home-page "https://bioconductor.org/packages/ChIPComp")
1731 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1733 "ChIPComp implements a statistical method for quantitative comparison of
1734 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1735 sites across multiple conditions considering matching control in ChIP-seq
1737 ;; Any version of the GPL.
1738 (license license:gpl3+)))
1740 (define-public r-riboprofiling
1742 (name "r-riboprofiling")
1747 (uri (bioconductor-uri "RiboProfiling" version))
1750 "0nfzyiq7cd6fs5agzl1zyfg8s631wi7kjngiyvd3vxlhi8wsjicx"))))
1751 (properties `((upstream-name . "RiboProfiling")))
1752 (build-system r-build-system)
1754 `(("r-biocgenerics" ,r-biocgenerics)
1755 ("r-biostrings" ,r-biostrings)
1756 ("r-data-table" ,r-data-table)
1757 ("r-genomeinfodb" ,r-genomeinfodb)
1758 ("r-genomicalignments" ,r-genomicalignments)
1759 ("r-genomicfeatures" ,r-genomicfeatures)
1760 ("r-genomicranges" ,r-genomicranges)
1761 ("r-ggbio" ,r-ggbio)
1762 ("r-ggplot2" ,r-ggplot2)
1763 ("r-iranges" ,r-iranges)
1765 ("r-reshape2" ,r-reshape2)
1766 ("r-rsamtools" ,r-rsamtools)
1767 ("r-rtracklayer" ,r-rtracklayer)
1768 ("r-s4vectors" ,r-s4vectors)
1769 ("r-sqldf" ,r-sqldf)))
1770 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1771 (synopsis "Ribosome profiling data analysis")
1772 (description "Starting with a BAM file, this package provides the
1773 necessary functions for quality assessment, read start position recalibration,
1774 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1775 of count data: pairs, log fold-change, codon frequency and coverage
1776 assessment, principal component analysis on codon coverage.")
1777 (license license:gpl3)))
1779 (define-public r-riboseqr
1786 (uri (bioconductor-uri "riboSeqR" version))
1789 "1jr7h64hyhyf9gf15lah6iqwyljfc8mraf9kya4lql6lcjjkjiqm"))))
1790 (properties `((upstream-name . "riboSeqR")))
1791 (build-system r-build-system)
1793 `(("r-abind" ,r-abind)
1794 ("r-bayseq" ,r-bayseq)
1795 ("r-genomeinfodb" ,r-genomeinfodb)
1796 ("r-genomicranges" ,r-genomicranges)
1797 ("r-iranges" ,r-iranges)
1798 ("r-rsamtools" ,r-rsamtools)
1799 ("r-seqlogo" ,r-seqlogo)))
1800 (home-page "https://bioconductor.org/packages/riboSeqR/")
1801 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1803 "This package provides plotting functions, frameshift detection and
1804 parsing of genetic sequencing data from ribosome profiling experiments.")
1805 (license license:gpl3)))
1807 (define-public r-interactionset
1809 (name "r-interactionset")
1814 (uri (bioconductor-uri "InteractionSet" version))
1817 "0n2l95h56x5g68p10cap8p4x3a6vaph2hjlk09vmi3j48lrzb2kh"))))
1819 `((upstream-name . "InteractionSet")))
1820 (build-system r-build-system)
1822 `(("r-biocgenerics" ,r-biocgenerics)
1823 ("r-genomeinfodb" ,r-genomeinfodb)
1824 ("r-genomicranges" ,r-genomicranges)
1825 ("r-iranges" ,r-iranges)
1826 ("r-matrix" ,r-matrix)
1828 ("r-s4vectors" ,r-s4vectors)
1829 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1830 (home-page "https://bioconductor.org/packages/InteractionSet")
1831 (synopsis "Base classes for storing genomic interaction data")
1833 "This package provides the @code{GInteractions},
1834 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1835 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1837 (license license:gpl3)))
1839 (define-public r-genomicinteractions
1841 (name "r-genomicinteractions")
1846 (uri (bioconductor-uri "GenomicInteractions" version))
1849 "10kwb70c9aq0bfqpq48h186lsbwgrg18m14r9z8x6n8l7cds5azc"))))
1851 `((upstream-name . "GenomicInteractions")))
1852 (build-system r-build-system)
1854 `(("r-biobase" ,r-biobase)
1855 ("r-biocgenerics" ,r-biocgenerics)
1856 ("r-data-table" ,r-data-table)
1857 ("r-dplyr" ,r-dplyr)
1858 ("r-genomeinfodb" ,r-genomeinfodb)
1859 ("r-genomicranges" ,r-genomicranges)
1860 ("r-ggplot2" ,r-ggplot2)
1861 ("r-gridextra" ,r-gridextra)
1863 ("r-igraph" ,r-igraph)
1864 ("r-interactionset" ,r-interactionset)
1865 ("r-iranges" ,r-iranges)
1866 ("r-rsamtools" ,r-rsamtools)
1867 ("r-rtracklayer" ,r-rtracklayer)
1868 ("r-s4vectors" ,r-s4vectors)
1869 ("r-stringr" ,r-stringr)))
1870 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1871 (synopsis "R package for handling genomic interaction data")
1873 "This R package provides tools for handling genomic interaction data,
1874 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1875 information and producing various plots and statistics.")
1876 (license license:gpl3)))
1878 (define-public r-ctc
1885 (uri (bioconductor-uri "ctc" version))
1888 "0wh27izkyr1j26nznisw654mb5c94xpwjjkx7r6bhwg9ihxxcl6d"))))
1889 (build-system r-build-system)
1890 (propagated-inputs `(("r-amap" ,r-amap)))
1891 (home-page "https://bioconductor.org/packages/ctc/")
1892 (synopsis "Cluster and tree conversion")
1894 "This package provides tools for exporting and importing classification
1895 trees and clusters to other programs.")
1896 (license license:gpl2)))
1898 (define-public r-goseq
1905 (uri (bioconductor-uri "goseq" version))
1908 "11ypa41qv1nx3cncxlwlbhdxqlwq95rb9byv2z3crrf9nfp24byv"))))
1909 (build-system r-build-system)
1911 `(("r-annotationdbi" ,r-annotationdbi)
1912 ("r-biasedurn" ,r-biasedurn)
1913 ("r-biocgenerics" ,r-biocgenerics)
1914 ("r-genelendatabase" ,r-genelendatabase)
1915 ("r-go-db" ,r-go-db)
1916 ("r-mgcv" ,r-mgcv)))
1917 (home-page "https://bioconductor.org/packages/goseq/")
1918 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1920 "This package provides tools to detect Gene Ontology and/or other user
1921 defined categories which are over/under represented in RNA-seq data.")
1922 (license license:lgpl2.0+)))
1924 (define-public r-glimma
1931 (uri (bioconductor-uri "Glimma" version))
1934 "1rjrqgl96iz4b3xqpc174wgz7bqmc8gbm9ljag0y27kz29fwng8r"))))
1935 (properties `((upstream-name . "Glimma")))
1936 (build-system r-build-system)
1938 `(("r-edger" ,r-edger)
1939 ("r-jsonlite" ,r-jsonlite)
1940 ("r-s4vectors" ,r-s4vectors)))
1941 (home-page "https://github.com/Shians/Glimma")
1942 (synopsis "Interactive HTML graphics")
1944 "This package generates interactive visualisations for analysis of
1945 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1946 HTML page. The interactions are built on top of the popular static
1947 representations of analysis results in order to provide additional
1949 (license license:lgpl3)))
1951 (define-public r-rots
1958 (uri (bioconductor-uri "ROTS" version))
1961 "08mwlb0lpprys2b7vif8aj5bnprmn09mm79zz158gbhrv9j9d1qm"))))
1962 (properties `((upstream-name . "ROTS")))
1963 (build-system r-build-system)
1965 `(("r-biobase" ,r-biobase)
1966 ("r-rcpp" ,r-rcpp)))
1967 (home-page "https://bioconductor.org/packages/ROTS/")
1968 (synopsis "Reproducibility-Optimized Test Statistic")
1970 "This package provides tools for calculating the
1971 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1973 (license license:gpl2+)))
1975 (define-public r-plgem
1982 (uri (bioconductor-uri "plgem" version))
1985 "0fkyvcw2qxp4g527s9rzia45yapi0r6gbij7svisil8rbgfdp45v"))))
1986 (build-system r-build-system)
1988 `(("r-biobase" ,r-biobase)
1989 ("r-mass" ,r-mass)))
1990 (home-page "http://www.genopolis.it")
1991 (synopsis "Detect differential expression in microarray and proteomics datasets")
1993 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1994 model the variance-versus-mean dependence that exists in a variety of
1995 genome-wide datasets, including microarray and proteomics data. The use of
1996 PLGEM has been shown to improve the detection of differentially expressed
1997 genes or proteins in these datasets.")
1998 (license license:gpl2)))
2000 (define-public r-inspect
2007 (uri (bioconductor-uri "INSPEcT" version))
2010 "1g8la7k4pnyr2hvk4yjd1bwvjy6nqbbb0fwxrrh2ifgqf4h21x2p"))))
2011 (properties `((upstream-name . "INSPEcT")))
2012 (build-system r-build-system)
2014 `(("r-biobase" ,r-biobase)
2015 ("r-biocgenerics" ,r-biocgenerics)
2016 ("r-biocparallel" ,r-biocparallel)
2017 ("r-deseq2" ,r-deseq2)
2018 ("r-desolve" ,r-desolve)
2019 ("r-gdata" ,r-gdata)
2020 ("r-genomeinfodb" ,r-genomeinfodb)
2021 ("r-genomicalignments" ,r-genomicalignments)
2022 ("r-genomicfeatures" ,r-genomicfeatures)
2023 ("r-genomicranges" ,r-genomicranges)
2024 ("r-iranges" ,r-iranges)
2025 ("r-kernsmooth" ,r-kernsmooth)
2026 ("r-plgem" ,r-plgem)
2028 ("r-rootsolve" ,r-rootsolve)
2029 ("r-rsamtools" ,r-rsamtools)
2030 ("r-s4vectors" ,r-s4vectors)
2031 ("r-shiny" ,r-shiny)
2032 ("r-summarizedexperiment" ,r-summarizedexperiment)
2033 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2034 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2035 (home-page "https://bioconductor.org/packages/INSPEcT")
2036 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2038 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2039 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2040 order to evaluate synthesis, processing and degradation rates and assess via
2041 modeling the rates that determines changes in mature mRNA levels.")
2042 (license license:gpl2)))
2044 (define-public r-dnabarcodes
2046 (name "r-dnabarcodes")
2051 (uri (bioconductor-uri "DNABarcodes" version))
2054 "0r2r9qc2qvf7rfl1h5ynvv3xd7n444zbc697s85qxqdpr4sxqmfd"))))
2055 (properties `((upstream-name . "DNABarcodes")))
2056 (build-system r-build-system)
2059 ("r-matrix" ,r-matrix)
2060 ("r-rcpp" ,r-rcpp)))
2061 (home-page "https://bioconductor.org/packages/DNABarcodes")
2062 (synopsis "Create and analyze DNA barcodes")
2064 "This package offers tools to create DNA barcode sets capable of
2065 correcting insertion, deletion, and substitution errors. Existing barcodes
2066 can be analyzed regarding their minimal, maximal and average distances between
2067 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2068 demultiplexed, i.e. assigned to their original reference barcode.")
2069 (license license:gpl2)))
2071 (define-public r-ruvseq
2078 (uri (bioconductor-uri "RUVSeq" version))
2081 "1ipbbzpngx988lsmwqv7vbmqm65m43xvsmipayfppkrr6jipzxrj"))))
2082 (properties `((upstream-name . "RUVSeq")))
2083 (build-system r-build-system)
2085 `(("r-biobase" ,r-biobase)
2086 ("r-edaseq" ,r-edaseq)
2087 ("r-edger" ,r-edger)
2088 ("r-mass" ,r-mass)))
2089 (home-page "https://github.com/drisso/RUVSeq")
2090 (synopsis "Remove unwanted variation from RNA-Seq data")
2092 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2093 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2095 (license license:artistic2.0)))
2097 (define-public r-biocneighbors
2099 (name "r-biocneighbors")
2104 (uri (bioconductor-uri "BiocNeighbors" version))
2107 "05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf"))))
2108 (properties `((upstream-name . "BiocNeighbors")))
2109 (build-system r-build-system)
2111 `(("r-biocparallel" ,r-biocparallel)
2112 ("r-matrix" ,r-matrix)
2114 ("r-rcppannoy" ,r-rcppannoy)
2115 ("r-rcpphnsw" ,r-rcpphnsw)
2116 ("r-s4vectors" ,r-s4vectors)))
2117 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2118 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2120 "This package implements exact and approximate methods for nearest
2121 neighbor detection, in a framework that allows them to be easily switched
2122 within Bioconductor packages or workflows. The exact algorithm is implemented
2123 using pre-clustering with the k-means algorithm. Functions are also provided
2124 to search for all neighbors within a given distance. Parallelization is
2125 achieved for all methods using the BiocParallel framework.")
2126 (license license:gpl3)))
2128 (define-public r-biocsingular
2130 (name "r-biocsingular")
2135 (uri (bioconductor-uri "BiocSingular" version))
2138 "0fjfmmpda7pszsck2hm7bp4509pl3xaz02q2q03d5vla62h1h81k"))))
2139 (properties `((upstream-name . "BiocSingular")))
2140 (build-system r-build-system)
2142 `(("r-beachmat" ,r-beachmat)
2143 ("r-biocgenerics" ,r-biocgenerics)
2144 ("r-biocparallel" ,r-biocparallel)
2145 ("r-delayedarray" ,r-delayedarray)
2146 ("r-irlba" ,r-irlba)
2147 ("r-matrix" ,r-matrix)
2150 ("r-s4vectors" ,r-s4vectors)))
2151 (home-page "https://github.com/LTLA/BiocSingular")
2152 (synopsis "Singular value decomposition for Bioconductor packages")
2154 "This package implements exact and approximate methods for singular value
2155 decomposition and principal components analysis, in a framework that allows
2156 them to be easily switched within Bioconductor packages or workflows. Where
2157 possible, parallelization is achieved using the BiocParallel framework.")
2158 (license license:gpl3)))
2160 (define-public r-destiny
2167 (uri (bioconductor-uri "destiny" version))
2170 "0vj9nk8g6i4vzm6cnzvbsqcvyk6fhmx0a0nxxrciarffyhqk81yz"))))
2171 (build-system r-build-system)
2173 `(("r-biobase" ,r-biobase)
2174 ("r-biocgenerics" ,r-biocgenerics)
2175 ("r-ggplot-multistats" ,r-ggplot-multistats)
2176 ("r-ggplot2" ,r-ggplot2)
2177 ("r-ggthemes" ,r-ggthemes)
2178 ("r-irlba" ,r-irlba)
2179 ("r-knn-covertree" ,r-knn-covertree)
2180 ("r-matrix" ,r-matrix)
2181 ("r-pcamethods" ,r-pcamethods)
2182 ("r-proxy" ,r-proxy)
2184 ("r-rcppeigen" ,r-rcppeigen)
2185 ("r-rcpphnsw" ,r-rcpphnsw)
2186 ("r-rspectra" ,r-rspectra)
2187 ("r-scales" ,r-scales)
2188 ("r-scatterplot3d" ,r-scatterplot3d)
2189 ("r-singlecellexperiment" ,r-singlecellexperiment)
2190 ("r-smoother" ,r-smoother)
2191 ("r-summarizedexperiment" ,r-summarizedexperiment)
2192 ("r-tidyr" ,r-tidyr)
2193 ("r-tidyselect" ,r-tidyselect)
2195 (home-page "https://bioconductor.org/packages/destiny/")
2196 (synopsis "Create and plot diffusion maps")
2197 (description "This package provides tools to create and plot diffusion
2199 ;; Any version of the GPL
2200 (license license:gpl3+)))
2202 (define-public r-savr
2209 (uri (bioconductor-uri "savR" version))
2212 "1lsnqjl6qxbj0wai05qb2wrxrhxq5iarv2livmvwiwv70iigqygf"))))
2213 (properties `((upstream-name . "savR")))
2214 (build-system r-build-system)
2216 `(("r-ggplot2" ,r-ggplot2)
2217 ("r-gridextra" ,r-gridextra)
2218 ("r-reshape2" ,r-reshape2)
2219 ("r-scales" ,r-scales)
2221 (home-page "https://github.com/bcalder/savR")
2222 (synopsis "Parse and analyze Illumina SAV files")
2224 "This package provides tools to parse Illumina Sequence Analysis
2225 Viewer (SAV) files, access data, and generate QC plots.")
2226 (license license:agpl3+)))
2228 (define-public r-chipexoqual
2230 (name "r-chipexoqual")
2235 (uri (bioconductor-uri "ChIPexoQual" version))
2238 "044n6kn16qczpdhp0w0z5x8xpr0rfs9s8q70rafgnvj7a2q1xdd0"))))
2239 (properties `((upstream-name . "ChIPexoQual")))
2240 (build-system r-build-system)
2242 `(("r-biocparallel" ,r-biocparallel)
2243 ("r-biovizbase" ,r-biovizbase)
2244 ("r-broom" ,r-broom)
2245 ("r-data-table" ,r-data-table)
2246 ("r-dplyr" ,r-dplyr)
2247 ("r-genomeinfodb" ,r-genomeinfodb)
2248 ("r-genomicalignments" ,r-genomicalignments)
2249 ("r-genomicranges" ,r-genomicranges)
2250 ("r-ggplot2" ,r-ggplot2)
2251 ("r-hexbin" ,r-hexbin)
2252 ("r-iranges" ,r-iranges)
2253 ("r-rcolorbrewer" ,r-rcolorbrewer)
2254 ("r-rmarkdown" ,r-rmarkdown)
2255 ("r-rsamtools" ,r-rsamtools)
2256 ("r-s4vectors" ,r-s4vectors)
2257 ("r-scales" ,r-scales)
2258 ("r-viridis" ,r-viridis)))
2259 (home-page "https://github.com/keleslab/ChIPexoQual")
2260 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2262 "This package provides a quality control pipeline for ChIP-exo/nexus
2264 (license license:gpl2+)))
2266 (define-public r-copynumber
2268 (name "r-copynumber")
2272 (uri (bioconductor-uri "copynumber" version))
2275 "0r6r1adj20x3ckm0dlipxlf1rzngr92xsxxpy81mqxf4jpmyr8gj"))))
2276 (build-system r-build-system)
2278 `(("r-s4vectors" ,r-s4vectors)
2279 ("r-iranges" ,r-iranges)
2280 ("r-genomicranges" ,r-genomicranges)
2281 ("r-biocgenerics" ,r-biocgenerics)))
2282 (home-page "https://bioconductor.org/packages/copynumber")
2283 (synopsis "Segmentation of single- and multi-track copy number data")
2285 "This package segments single- and multi-track copy number data by a
2286 penalized least squares regression method.")
2287 (license license:artistic2.0)))
2289 (define-public r-dnacopy
2296 (uri (bioconductor-uri "DNAcopy" version))
2299 "119z5lqhhw9ppg6s4dvbxk1kxf3wc55ibpm9b88c91s04yd7m9yw"))))
2300 (properties `((upstream-name . "DNAcopy")))
2301 (build-system r-build-system)
2302 (native-inputs `(("gfortran" ,gfortran)))
2303 (home-page "https://bioconductor.org/packages/DNAcopy")
2304 (synopsis "DNA copy number data analysis")
2306 "This package implements the @dfn{circular binary segmentation} (CBS)
2307 algorithm to segment DNA copy number data and identify genomic regions with
2308 abnormal copy number.")
2309 (license license:gpl2+)))
2311 ;; This is a CRAN package, but it uncharacteristically depends on a
2312 ;; Bioconductor package.
2313 (define-public r-htscluster
2315 (name "r-htscluster")
2320 (uri (cran-uri "HTSCluster" version))
2323 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2324 (properties `((upstream-name . "HTSCluster")))
2325 (build-system r-build-system)
2327 `(("r-capushe" ,r-capushe)
2328 ("r-edger" ,r-edger)
2329 ("r-plotrix" ,r-plotrix)))
2330 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2331 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2333 "This package provides a Poisson mixture model is implemented to cluster
2334 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2335 estimation is performed using either the EM or CEM algorithm, and the slope
2336 heuristics are used for model selection (i.e., to choose the number of
2338 (license license:gpl3+)))
2340 (define-public r-deds
2347 (uri (bioconductor-uri "DEDS" version))
2350 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
2351 (properties `((upstream-name . "DEDS")))
2352 (build-system r-build-system)
2353 (home-page "https://bioconductor.org/packages/DEDS/")
2354 (synopsis "Differential expression via distance summary for microarray data")
2356 "This library contains functions that calculate various statistics of
2357 differential expression for microarray data, including t statistics, fold
2358 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2359 also implements a new methodology called DEDS (Differential Expression via
2360 Distance Summary), which selects differentially expressed genes by integrating
2361 and summarizing a set of statistics using a weighted distance approach.")
2362 ;; Any version of the LGPL.
2363 (license license:lgpl3+)))
2365 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2367 (define-public r-nbpseq
2374 (uri (cran-uri "NBPSeq" version))
2377 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2378 (properties `((upstream-name . "NBPSeq")))
2379 (build-system r-build-system)
2381 `(("r-qvalue" ,r-qvalue)))
2382 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2383 (synopsis "Negative binomial models for RNA-Seq data")
2385 "This package provides negative binomial models for two-group comparisons
2386 and regression inferences from RNA-sequencing data.")
2387 (license license:gpl2)))
2389 (define-public r-ebseq
2396 (uri (bioconductor-uri "EBSeq" version))
2399 "0ay1vcccpc29r3vinlnwp9256345bfb346kg2y11kib4bnrabjb6"))))
2400 (properties `((upstream-name . "EBSeq")))
2401 (build-system r-build-system)
2403 `(("r-blockmodeling" ,r-blockmodeling)
2404 ("r-gplots" ,r-gplots)
2405 ("r-testthat" ,r-testthat)))
2406 (home-page "https://bioconductor.org/packages/EBSeq")
2407 (synopsis "Differential expression analysis of RNA-seq data")
2409 "This package provides tools for differential expression analysis at both
2410 gene and isoform level using RNA-seq data")
2411 (license license:artistic2.0)))
2413 (define-public r-lpsymphony
2415 (name "r-lpsymphony")
2420 (uri (bioconductor-uri "lpsymphony" version))
2423 "0j5j9kggh3l61vp6hpnqf45d5kzifksaj0sqhvs1zahmx2c1gfdv"))))
2424 (build-system r-build-system)
2426 `(("gfortran" ,gfortran)
2429 `(("pkg-config" ,pkg-config)))
2430 (home-page "http://r-forge.r-project.org/projects/rsymphony")
2431 (synopsis "Symphony integer linear programming solver in R")
2433 "This package was derived from Rsymphony. The package provides an R
2434 interface to SYMPHONY, a linear programming solver written in C++. The main
2435 difference between this package and Rsymphony is that it includes the solver
2436 source code, while Rsymphony expects to find header and library files on the
2437 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2438 to install interface to SYMPHONY.")
2439 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2440 ;; lpsimphony is released under the same terms.
2441 (license license:epl1.0)))
2443 (define-public r-ihw
2450 (uri (bioconductor-uri "IHW" version))
2453 "0rnw7r9pylpj3a5graavcpiqv2v67rv2a4dlcynkf4ihpxs4bg8x"))))
2454 (properties `((upstream-name . "IHW")))
2455 (build-system r-build-system)
2457 `(("r-biocgenerics" ,r-biocgenerics)
2458 ("r-fdrtool" ,r-fdrtool)
2459 ("r-lpsymphony" ,r-lpsymphony)
2460 ("r-slam" ,r-slam)))
2461 (home-page "https://bioconductor.org/packages/IHW")
2462 (synopsis "Independent hypothesis weighting")
2464 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2465 procedure that increases power compared to the method of Benjamini and
2466 Hochberg by assigning data-driven weights to each hypothesis. The input to
2467 IHW is a two-column table of p-values and covariates. The covariate can be
2468 any continuous-valued or categorical variable that is thought to be
2469 informative on the statistical properties of each hypothesis test, while it is
2470 independent of the p-value under the null hypothesis.")
2471 (license license:artistic2.0)))
2473 (define-public r-icobra
2480 (uri (bioconductor-uri "iCOBRA" version))
2483 "1l0yr2grpwmr3pc5h50p1j4nxyb1ddmc55l7rhxpp4igh4fq1avz"))))
2484 (properties `((upstream-name . "iCOBRA")))
2485 (build-system r-build-system)
2487 `(("r-dplyr" ,r-dplyr)
2489 ("r-ggplot2" ,r-ggplot2)
2490 ("r-limma" ,r-limma)
2491 ("r-reshape2" ,r-reshape2)
2493 ("r-scales" ,r-scales)
2494 ("r-shiny" ,r-shiny)
2495 ("r-shinybs" ,r-shinybs)
2496 ("r-shinydashboard" ,r-shinydashboard)
2497 ("r-upsetr" ,r-upsetr)))
2498 (home-page "https://bioconductor.org/packages/iCOBRA")
2499 (synopsis "Comparison and visualization of ranking and assignment methods")
2501 "This package provides functions for calculation and visualization of
2502 performance metrics for evaluation of ranking and binary
2503 classification (assignment) methods. It also contains a Shiny application for
2504 interactive exploration of results.")
2505 (license license:gpl2+)))
2507 (define-public r-mast
2514 (uri (bioconductor-uri "MAST" version))
2517 "1l78rrwkzyswpj6pgc9z8290fqrk4akba76invkkazpyh91r8gga"))))
2518 (properties `((upstream-name . "MAST")))
2519 (build-system r-build-system)
2521 `(("r-abind" ,r-abind)
2522 ("r-biobase" ,r-biobase)
2523 ("r-biocgenerics" ,r-biocgenerics)
2524 ("r-data-table" ,r-data-table)
2525 ("r-ggplot2" ,r-ggplot2)
2527 ("r-progress" ,r-progress)
2528 ("r-reshape2" ,r-reshape2)
2529 ("r-s4vectors" ,r-s4vectors)
2530 ("r-singlecellexperiment" ,r-singlecellexperiment)
2531 ("r-stringr" ,r-stringr)
2532 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2533 (home-page "https://github.com/RGLab/MAST/")
2534 (synopsis "Model-based analysis of single cell transcriptomics")
2536 "This package provides methods and models for handling zero-inflated
2537 single cell assay data.")
2538 (license license:gpl2+)))
2540 (define-public r-monocle
2547 (uri (bioconductor-uri "monocle" version))
2550 "18b9y592q48mbcp5w095qs1kaklq64v6dcnlpqhv3rwxvywygsz2"))))
2551 (build-system r-build-system)
2553 `(("r-biobase" ,r-biobase)
2554 ("r-biocgenerics" ,r-biocgenerics)
2555 ("r-biocviews" ,r-biocviews)
2556 ("r-cluster" ,r-cluster)
2557 ("r-combinat" ,r-combinat)
2558 ("r-ddrtree" ,r-ddrtree)
2559 ("r-densityclust" ,r-densityclust)
2560 ("r-dplyr" ,r-dplyr)
2561 ("r-fastica" ,r-fastica)
2562 ("r-ggplot2" ,r-ggplot2)
2563 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2564 ("r-igraph" ,r-igraph)
2565 ("r-irlba" ,r-irlba)
2566 ("r-limma" ,r-limma)
2568 ("r-matrix" ,r-matrix)
2569 ("r-matrixstats" ,r-matrixstats)
2570 ("r-pheatmap" ,r-pheatmap)
2572 ("r-proxy" ,r-proxy)
2573 ("r-qlcmatrix" ,r-qlcmatrix)
2576 ("r-reshape2" ,r-reshape2)
2577 ("r-rtsne" ,r-rtsne)
2579 ("r-stringr" ,r-stringr)
2580 ("r-tibble" ,r-tibble)
2582 ("r-viridis" ,r-viridis)))
2583 (home-page "https://bioconductor.org/packages/monocle")
2584 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2586 "Monocle performs differential expression and time-series analysis for
2587 single-cell expression experiments. It orders individual cells according to
2588 progress through a biological process, without knowing ahead of time which
2589 genes define progress through that process. Monocle also performs
2590 differential expression analysis, clustering, visualization, and other useful
2591 tasks on single cell expression data. It is designed to work with RNA-Seq and
2592 qPCR data, but could be used with other types as well.")
2593 (license license:artistic2.0)))
2595 (define-public r-monocle3
2603 (url "https://github.com/cole-trapnell-lab/monocle3.git")
2605 (file-name (git-file-name name version))
2608 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2609 (build-system r-build-system)
2611 `(("r-biobase" ,r-biobase)
2612 ("r-biocgenerics" ,r-biocgenerics)
2613 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2614 ("r-dplyr" ,r-dplyr)
2615 ("r-ggplot2" ,r-ggplot2)
2616 ("r-ggrepel" ,r-ggrepel)
2618 ("r-htmlwidgets" ,r-htmlwidgets)
2619 ("r-igraph" ,r-igraph)
2620 ("r-irlba" ,r-irlba)
2621 ("r-limma" ,r-limma)
2622 ("r-lmtest" ,r-lmtest)
2624 ("r-matrix" ,r-matrix)
2625 ("r-matrix-utils" ,r-matrix-utils)
2626 ("r-pbapply" ,r-pbapply)
2627 ("r-pbmcapply" ,r-pbmcapply)
2628 ("r-pheatmap" ,r-pheatmap)
2629 ("r-plotly" ,r-plotly)
2631 ("r-proxy" ,r-proxy)
2633 ("r-purrr" ,r-purrr)
2636 ("r-rcppparallel" ,r-rcppparallel)
2637 ("r-reshape2" ,r-reshape2)
2638 ("r-reticulate" ,r-reticulate)
2639 ("r-rhpcblasctl" ,r-rhpcblasctl)
2640 ("r-rtsne" ,r-rtsne)
2641 ("r-shiny" ,r-shiny)
2643 ("r-spdep" ,r-spdep)
2644 ("r-speedglm" ,r-speedglm)
2645 ("r-stringr" ,r-stringr)
2646 ("r-singlecellexperiment" ,r-singlecellexperiment)
2647 ("r-tibble" ,r-tibble)
2648 ("r-tidyr" ,r-tidyr)
2650 ("r-viridis" ,r-viridis)))
2651 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2652 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2654 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2655 (license license:expat)))
2657 (define-public r-noiseq
2664 (uri (bioconductor-uri "NOISeq" version))
2667 "1a8p66hhnwmay0rjabwq7356wr93yn33nqgr9rr7whpp9nls1hg4"))))
2668 (properties `((upstream-name . "NOISeq")))
2669 (build-system r-build-system)
2671 `(("r-biobase" ,r-biobase)
2672 ("r-matrix" ,r-matrix)))
2673 (home-page "https://bioconductor.org/packages/NOISeq")
2674 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2676 "This package provides tools to support the analysis of RNA-seq
2677 expression data or other similar kind of data. It provides exploratory plots
2678 to evaluate saturation, count distribution, expression per chromosome, type of
2679 detected features, features length, etc. It also supports the analysis of
2680 differential expression between two experimental conditions with no parametric
2682 (license license:artistic2.0)))
2684 (define-public r-scdd
2691 (uri (bioconductor-uri "scDD" version))
2694 "0nk0qq664zs7dnlcamdkrrhvll01p7f96jj3igbxxlzj3dvr58w4"))))
2695 (properties `((upstream-name . "scDD")))
2696 (build-system r-build-system)
2699 ("r-biocparallel" ,r-biocparallel)
2700 ("r-ebseq" ,r-ebseq)
2701 ("r-fields" ,r-fields)
2702 ("r-ggplot2" ,r-ggplot2)
2703 ("r-mclust" ,r-mclust)
2704 ("r-outliers" ,r-outliers)
2705 ("r-s4vectors" ,r-s4vectors)
2706 ("r-scran" ,r-scran)
2707 ("r-singlecellexperiment" ,r-singlecellexperiment)
2708 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2709 (home-page "https://github.com/kdkorthauer/scDD")
2710 (synopsis "Mixture modeling of single-cell RNA-seq data")
2712 "This package implements a method to analyze single-cell RNA-seq data
2713 utilizing flexible Dirichlet Process mixture models. Genes with differential
2714 distributions of expression are classified into several interesting patterns
2715 of differences between two conditions. The package also includes functions
2716 for simulating data with these patterns from negative binomial
2718 (license license:gpl2)))
2720 (define-public r-scone
2727 (uri (bioconductor-uri "scone" version))
2730 "1hfsbnix0y9ad6bj0d8q2aw13pb3vjcaa0dfwxxapzl90zwbsjhp"))))
2731 (build-system r-build-system)
2733 `(("r-aroma-light" ,r-aroma-light)
2734 ("r-biocparallel" ,r-biocparallel)
2736 ("r-class" ,r-class)
2737 ("r-cluster" ,r-cluster)
2738 ("r-compositions" ,r-compositions)
2739 ("r-diptest" ,r-diptest)
2740 ("r-edger" ,r-edger)
2742 ("r-gplots" ,r-gplots)
2743 ("r-hexbin" ,r-hexbin)
2744 ("r-limma" ,r-limma)
2745 ("r-matrixstats" ,r-matrixstats)
2746 ("r-mixtools" ,r-mixtools)
2747 ("r-rarpack" ,r-rarpack)
2748 ("r-rcolorbrewer" ,r-rcolorbrewer)
2749 ("r-rhdf5" ,r-rhdf5)
2750 ("r-ruvseq" ,r-ruvseq)
2751 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2752 (home-page "https://bioconductor.org/packages/scone")
2753 (synopsis "Single cell overview of normalized expression data")
2755 "SCONE is an R package for comparing and ranking the performance of
2756 different normalization schemes for single-cell RNA-seq and other
2757 high-throughput analyses.")
2758 (license license:artistic2.0)))
2760 (define-public r-geoquery
2767 (uri (bioconductor-uri "GEOquery" version))
2770 "0j8mlldy7dc38fx5zwj6z6l4b9bhvrn8sil3z8asnd4ic7w9ifx5"))))
2771 (properties `((upstream-name . "GEOquery")))
2772 (build-system r-build-system)
2774 `(("r-biobase" ,r-biobase)
2775 ("r-dplyr" ,r-dplyr)
2777 ("r-limma" ,r-limma)
2778 ("r-magrittr" ,r-magrittr)
2779 ("r-readr" ,r-readr)
2780 ("r-tidyr" ,r-tidyr)
2781 ("r-xml2" ,r-xml2)))
2782 (home-page "https://github.com/seandavi/GEOquery/")
2783 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2785 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2786 microarray data. Given the rich and varied nature of this resource, it is
2787 only natural to want to apply BioConductor tools to these data. GEOquery is
2788 the bridge between GEO and BioConductor.")
2789 (license license:gpl2)))
2791 (define-public r-illuminaio
2793 (name "r-illuminaio")
2798 (uri (bioconductor-uri "illuminaio" version))
2801 "1psza8jq6h8fv2rm91ah67dgjlnj1l80yracwgdl1agd0ycv90sh"))))
2802 (build-system r-build-system)
2804 `(("r-base64" ,r-base64)))
2805 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2806 (synopsis "Parse Illumina microarray output files")
2808 "This package provides tools for parsing Illumina's microarray output
2809 files, including IDAT.")
2810 (license license:gpl2)))
2812 (define-public r-siggenes
2819 (uri (bioconductor-uri "siggenes" version))
2822 "03lmq3hqprwps4miynl2vhqi3v4als5vqmz4lb19lk5a4zja72b4"))))
2823 (build-system r-build-system)
2825 `(("r-biobase" ,r-biobase)
2826 ("r-multtest" ,r-multtest)
2827 ("r-scrime" ,r-scrime)))
2828 (home-page "https://bioconductor.org/packages/siggenes/")
2830 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2832 "This package provides tools for the identification of differentially
2833 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2834 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2835 Bayes Analyses of Microarrays} (EBAM).")
2836 (license license:lgpl2.0+)))
2838 (define-public r-bumphunter
2840 (name "r-bumphunter")
2845 (uri (bioconductor-uri "bumphunter" version))
2848 "1p3gwb954zns61d1pwgkplxnvgk2lixrl93kkkf439wa3vlgsnjv"))))
2849 (build-system r-build-system)
2851 `(("r-annotationdbi" ,r-annotationdbi)
2852 ("r-biocgenerics" ,r-biocgenerics)
2853 ("r-dorng" ,r-dorng)
2854 ("r-foreach" ,r-foreach)
2855 ("r-genomeinfodb" ,r-genomeinfodb)
2856 ("r-genomicfeatures" ,r-genomicfeatures)
2857 ("r-genomicranges" ,r-genomicranges)
2858 ("r-iranges" ,r-iranges)
2859 ("r-iterators" ,r-iterators)
2860 ("r-limma" ,r-limma)
2861 ("r-locfit" ,r-locfit)
2862 ("r-matrixstats" ,r-matrixstats)
2863 ("r-s4vectors" ,r-s4vectors)))
2864 (home-page "https://github.com/ririzarr/bumphunter")
2865 (synopsis "Find bumps in genomic data")
2867 "This package provides tools for finding bumps in genomic data in order
2868 to identify differentially methylated regions in epigenetic epidemiology
2870 (license license:artistic2.0)))
2872 (define-public r-minfi
2879 (uri (bioconductor-uri "minfi" version))
2882 "177isdvcq2476xybvfbh7x11qsj5nzckgh3b6p156wlx9ap9dvl3"))))
2883 (build-system r-build-system)
2885 `(("r-beanplot" ,r-beanplot)
2886 ("r-biobase" ,r-biobase)
2887 ("r-biocgenerics" ,r-biocgenerics)
2888 ("r-biocparallel" ,r-biocparallel)
2889 ("r-biostrings" ,r-biostrings)
2890 ("r-bumphunter" ,r-bumphunter)
2891 ("r-data-table" ,r-data-table)
2892 ("r-delayedarray" ,r-delayedarray)
2893 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2894 ("r-genefilter" ,r-genefilter)
2895 ("r-genomeinfodb" ,r-genomeinfodb)
2896 ("r-genomicranges" ,r-genomicranges)
2897 ("r-geoquery" ,r-geoquery)
2898 ("r-hdf5array" ,r-hdf5array)
2899 ("r-illuminaio" ,r-illuminaio)
2900 ("r-iranges" ,r-iranges)
2901 ("r-lattice" ,r-lattice)
2902 ("r-limma" ,r-limma)
2904 ("r-mclust" ,r-mclust)
2906 ("r-nor1mix" ,r-nor1mix)
2907 ("r-preprocesscore" ,r-preprocesscore)
2908 ("r-quadprog" ,r-quadprog)
2909 ("r-rcolorbrewer" ,r-rcolorbrewer)
2910 ("r-reshape" ,r-reshape)
2911 ("r-s4vectors" ,r-s4vectors)
2912 ("r-siggenes" ,r-siggenes)
2913 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2914 (home-page "https://github.com/hansenlab/minfi")
2915 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2917 "This package provides tools to analyze and visualize Illumina Infinium
2918 methylation arrays.")
2919 (license license:artistic2.0)))
2921 (define-public r-methylumi
2923 (name "r-methylumi")
2928 (uri (bioconductor-uri "methylumi" version))
2931 "0zd4h6n37v3z0mas69z2xsf5s0naih828987m8v0g9hhq4f6hf5w"))))
2932 (build-system r-build-system)
2934 `(("r-annotate" ,r-annotate)
2935 ("r-annotationdbi" ,r-annotationdbi)
2936 ("r-biobase" ,r-biobase)
2937 ("r-biocgenerics" ,r-biocgenerics)
2938 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2939 ("r-genefilter" ,r-genefilter)
2940 ("r-genomeinfodb" ,r-genomeinfodb)
2941 ("r-genomicranges" ,r-genomicranges)
2942 ("r-ggplot2" ,r-ggplot2)
2943 ("r-illuminaio" ,r-illuminaio)
2944 ("r-iranges" ,r-iranges)
2945 ("r-lattice" ,r-lattice)
2946 ("r-matrixstats" ,r-matrixstats)
2947 ("r-minfi" ,r-minfi)
2948 ("r-reshape2" ,r-reshape2)
2949 ("r-s4vectors" ,r-s4vectors)
2950 ("r-scales" ,r-scales)
2951 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2952 (home-page "https://bioconductor.org/packages/methylumi")
2953 (synopsis "Handle Illumina methylation data")
2955 "This package provides classes for holding and manipulating Illumina
2956 methylation data. Based on eSet, it can contain MIAME information, sample
2957 information, feature information, and multiple matrices of data. An
2958 \"intelligent\" import function, methylumiR can read the Illumina text files
2959 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2960 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2961 background correction, and quality control features for GoldenGate, Infinium,
2962 and Infinium HD arrays are also included.")
2963 (license license:gpl2)))
2965 (define-public r-lumi
2972 (uri (bioconductor-uri "lumi" version))
2975 "0lgrqbdvp7ykcafc0bpnbcsf396na3jj5c35x9ysf5bpcas23nmm"))))
2976 (build-system r-build-system)
2978 `(("r-affy" ,r-affy)
2979 ("r-annotate" ,r-annotate)
2980 ("r-annotationdbi" ,r-annotationdbi)
2981 ("r-biobase" ,r-biobase)
2983 ("r-genomicfeatures" ,r-genomicfeatures)
2984 ("r-genomicranges" ,r-genomicranges)
2985 ("r-kernsmooth" ,r-kernsmooth)
2986 ("r-lattice" ,r-lattice)
2988 ("r-methylumi" ,r-methylumi)
2990 ("r-nleqslv" ,r-nleqslv)
2991 ("r-preprocesscore" ,r-preprocesscore)
2992 ("r-rsqlite" ,r-rsqlite)))
2993 (home-page "https://bioconductor.org/packages/lumi")
2994 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2996 "The lumi package provides an integrated solution for the Illumina
2997 microarray data analysis. It includes functions of Illumina
2998 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2999 variance stabilization, normalization and gene annotation at the probe level.
3000 It also includes the functions of processing Illumina methylation microarrays,
3001 especially Illumina Infinium methylation microarrays.")
3002 (license license:lgpl2.0+)))
3004 (define-public r-linnorm
3011 (uri (bioconductor-uri "Linnorm" version))
3014 "15mhwiqmp9m65zvrdbr2hhy3x81lf4jbwgjsf75g41if2v2g8x67"))))
3015 (properties `((upstream-name . "Linnorm")))
3016 (build-system r-build-system)
3018 `(("r-amap" ,r-amap)
3019 ("r-apcluster" ,r-apcluster)
3020 ("r-ellipse" ,r-ellipse)
3021 ("r-fastcluster" ,r-fastcluster)
3023 ("r-ggdendro" ,r-ggdendro)
3024 ("r-ggplot2" ,r-ggplot2)
3025 ("r-gmodels" ,r-gmodels)
3026 ("r-igraph" ,r-igraph)
3027 ("r-limma" ,r-limma)
3029 ("r-mclust" ,r-mclust)
3031 ("r-rcpparmadillo" ,r-rcpparmadillo)
3032 ("r-rtsne" ,r-rtsne)
3033 ("r-statmod" ,r-statmod)
3034 ("r-vegan" ,r-vegan)
3036 (home-page "http://www.jjwanglab.org/Linnorm/")
3037 (synopsis "Linear model and normality based transformation method")
3039 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3040 count data or any large scale count data. It transforms such datasets for
3041 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3042 the following pipelines are implemented:
3045 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3046 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3047 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3048 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3049 @item Differential expression analysis or differential peak detection using
3050 limma (@code{Linnorm.limma})
3051 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3052 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3053 @item Stable gene selection for scRNA-seq data; for users without or who do
3054 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3055 @item Data imputation (@code{Linnorm.DataImput}).
3058 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3059 @code{RnaXSim} function is included for simulating RNA-seq data for the
3060 evaluation of DEG analysis methods.")
3061 (license license:expat)))
3063 (define-public r-ioniser
3070 (uri (bioconductor-uri "IONiseR" version))
3073 "1c265bzh923i9mw83mjpj0bzbkixbs6sg1h1z51y9xjkakdgg90f"))))
3074 (properties `((upstream-name . "IONiseR")))
3075 (build-system r-build-system)
3077 `(("r-biocgenerics" ,r-biocgenerics)
3078 ("r-biocparallel" ,r-biocparallel)
3079 ("r-biostrings" ,r-biostrings)
3080 ("r-bit64" ,r-bit64)
3081 ("r-dplyr" ,r-dplyr)
3082 ("r-ggplot2" ,r-ggplot2)
3083 ("r-magrittr" ,r-magrittr)
3084 ("r-rhdf5" ,r-rhdf5)
3085 ("r-shortread" ,r-shortread)
3086 ("r-stringr" ,r-stringr)
3087 ("r-tibble" ,r-tibble)
3088 ("r-tidyr" ,r-tidyr)
3089 ("r-xvector" ,r-xvector)))
3090 (home-page "https://bioconductor.org/packages/IONiseR/")
3091 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3093 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3094 MinION data. It extracts summary statistics from a set of fast5 files and can
3095 be used either before or after base calling. In addition to standard
3096 summaries of the read-types produced, it provides a number of plots for
3097 visualising metrics relative to experiment run time or spatially over the
3098 surface of a flowcell.")
3099 (license license:expat)))
3101 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3102 (define-public r-gkmsvm
3109 (uri (cran-uri "gkmSVM" version))
3112 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
3113 (properties `((upstream-name . "gkmSVM")))
3114 (build-system r-build-system)
3116 `(("r-biocgenerics" ,r-biocgenerics)
3117 ("r-biostrings" ,r-biostrings)
3118 ("r-genomeinfodb" ,r-genomeinfodb)
3119 ("r-genomicranges" ,r-genomicranges)
3120 ("r-iranges" ,r-iranges)
3121 ("r-kernlab" ,r-kernlab)
3124 ("r-rtracklayer" ,r-rtracklayer)
3125 ("r-s4vectors" ,r-s4vectors)
3126 ("r-seqinr" ,r-seqinr)))
3127 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3128 (synopsis "Gapped-kmer support vector machine")
3130 "This R package provides tools for training gapped-kmer SVM classifiers
3131 for DNA and protein sequences. This package supports several sequence
3132 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3133 (license license:gpl2+)))
3135 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
3136 (define-public r-mutoss
3143 (uri (cran-uri "mutoss" version))
3146 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3147 (properties `((upstream-name . "mutoss")))
3148 (build-system r-build-system)
3150 `(("r-multcomp" ,r-multcomp)
3151 ("r-multtest" ,r-multtest)
3152 ("r-mvtnorm" ,r-mvtnorm)
3153 ("r-plotrix" ,r-plotrix)))
3154 (home-page "https://github.com/kornl/mutoss/")
3155 (synopsis "Unified multiple testing procedures")
3157 "This package is designed to ease the application and comparison of
3158 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3159 are standardized and usable by the accompanying mutossGUI package.")
3160 ;; Any version of the GPL.
3161 (license (list license:gpl2+ license:gpl3+))))
3163 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3164 ;; from Bioconductor, so we put it here.
3165 (define-public r-metap
3172 (uri (cran-uri "metap" version))
3175 "0pfbcixjrzx81l9wqhlp55khg9k63zf8pvg2n39c19akr4ppzhvf"))))
3176 (build-system r-build-system)
3178 `(("r-lattice" ,r-lattice)
3179 ("r-mutoss" ,r-mutoss)
3180 ("r-rdpack" ,r-rdpack)
3181 ("r-tfisher" ,r-tfisher)))
3182 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3183 (synopsis "Meta-analysis of significance values")
3185 "The canonical way to perform meta-analysis involves using effect sizes.
3186 When they are not available this package provides a number of methods for
3187 meta-analysis of significance values including the methods of Edgington,
3188 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3189 published results; and a routine for graphical display.")
3190 (license license:gpl2)))
3192 (define-public r-triform
3199 (uri (bioconductor-uri "triform" version))
3202 "12qdyrcw2mcawqdw65v0hjaghzlwa10xl6j8458izcrm5k6dlvz9"))))
3203 (build-system r-build-system)
3205 `(("r-biocgenerics" ,r-biocgenerics)
3206 ("r-iranges" ,r-iranges)
3207 ("r-yaml" ,r-yaml)))
3208 (home-page "https://bioconductor.org/packages/triform/")
3209 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3211 "The Triform algorithm uses model-free statistics to identify peak-like
3212 distributions of TF ChIP sequencing reads, taking advantage of an improved
3213 peak definition in combination with known profile characteristics.")
3214 (license license:gpl2)))
3216 (define-public r-varianttools
3218 (name "r-varianttools")
3223 (uri (bioconductor-uri "VariantTools" version))
3226 "0aafcprsqbn1xl8jqnxfl8r2d0lmzhssqpr26lam2cprh3yk0xiv"))))
3227 (properties `((upstream-name . "VariantTools")))
3228 (build-system r-build-system)
3230 `(("r-biobase" ,r-biobase)
3231 ("r-biocgenerics" ,r-biocgenerics)
3232 ("r-biocparallel" ,r-biocparallel)
3233 ("r-biostrings" ,r-biostrings)
3234 ("r-bsgenome" ,r-bsgenome)
3235 ("r-genomeinfodb" ,r-genomeinfodb)
3236 ("r-genomicfeatures" ,r-genomicfeatures)
3237 ("r-genomicranges" ,r-genomicranges)
3238 ("r-iranges" ,r-iranges)
3239 ("r-matrix" ,r-matrix)
3240 ("r-rsamtools" ,r-rsamtools)
3241 ("r-rtracklayer" ,r-rtracklayer)
3242 ("r-s4vectors" ,r-s4vectors)
3243 ("r-variantannotation" ,r-variantannotation)))
3244 (home-page "https://bioconductor.org/packages/VariantTools/")
3245 (synopsis "Tools for exploratory analysis of variant calls")
3247 "Explore, diagnose, and compare variant calls using filters. The
3248 VariantTools package supports a workflow for loading data, calling single
3249 sample variants and tumor-specific somatic mutations or other sample-specific
3250 variant types (e.g., RNA editing). Most of the functions operate on
3251 alignments (BAM files) or datasets of called variants. The user is expected
3252 to have already aligned the reads with a separate tool, e.g., GSNAP via
3254 (license license:artistic2.0)))
3256 (define-public r-heatplus
3263 (uri (bioconductor-uri "Heatplus" version))
3266 "0hx5gqgh4xrkx37ccprq7azj9jziff137bdk0gvrixcx52ws6h89"))))
3267 (properties `((upstream-name . "Heatplus")))
3268 (build-system r-build-system)
3270 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3271 (home-page "https://github.com/alexploner/Heatplus")
3272 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3274 "This package provides tools to display a rectangular heatmap (intensity
3275 plot) of a data matrix. By default, both samples (columns) and features (row)
3276 of the matrix are sorted according to a hierarchical clustering, and the
3277 corresponding dendrogram is plotted. Optionally, panels with additional
3278 information about samples and features can be added to the plot.")
3279 (license license:gpl2+)))
3281 (define-public r-gosemsim
3288 (uri (bioconductor-uri "GOSemSim" version))
3291 "0pqnlgdvh5szjhwc1mw1snjgpj9lrsnk44bn164cl3zwvdayccya"))))
3292 (properties `((upstream-name . "GOSemSim")))
3293 (build-system r-build-system)
3295 `(("r-annotationdbi" ,r-annotationdbi)
3296 ("r-go-db" ,r-go-db)
3297 ("r-rcpp" ,r-rcpp)))
3298 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3299 (synopsis "GO-terms semantic similarity measures")
3301 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3302 quantitative ways to compute similarities between genes and gene groups, and
3303 have became important basis for many bioinformatics analysis approaches.
3304 GOSemSim is an R package for semantic similarity computation among GO terms,
3305 sets of GO terms, gene products and gene clusters.")
3306 (license license:artistic2.0)))
3308 (define-public r-anota
3315 (uri (bioconductor-uri "anota" version))
3318 "1bkavzrxy1bjz0bwapwa9i3ysln7gljgziwd8c05fmg2f46j1z6m"))))
3319 (build-system r-build-system)
3321 `(("r-multtest" ,r-multtest)
3322 ("r-qvalue" ,r-qvalue)))
3323 (home-page "https://bioconductor.org/packages/anota/")
3324 (synopsis "Analysis of translational activity")
3326 "Genome wide studies of translational control is emerging as a tool to
3327 study various biological conditions. The output from such analysis is both
3328 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3329 involved in translation (the actively translating mRNA level) for each mRNA.
3330 The standard analysis of such data strives towards identifying differential
3331 translational between two or more sample classes - i.e. differences in
3332 actively translated mRNA levels that are independent of underlying differences
3333 in cytosolic mRNA levels. This package allows for such analysis using partial
3334 variances and the random variance model. As 10s of thousands of mRNAs are
3335 analyzed in parallel the library performs a number of tests to assure that
3336 the data set is suitable for such analysis.")
3337 (license license:gpl3)))
3339 (define-public r-sigpathway
3341 (name "r-sigpathway")
3346 (uri (bioconductor-uri "sigPathway" version))
3349 "057qdkbfldpy6hsysk9mrs1vvsqgyl9yx2s6c2f26jz1pardkbqb"))))
3350 (properties `((upstream-name . "sigPathway")))
3351 (build-system r-build-system)
3352 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3353 (synopsis "Pathway analysis")
3355 "This package is used to conduct pathway analysis by calculating the NT_k
3356 and NE_k statistics in a statistical framework for determining whether a
3357 specified group of genes for a pathway has a coordinated association with a
3358 phenotype of interest.")
3359 (license license:gpl2)))
3361 (define-public r-fgsea
3368 (uri (bioconductor-uri "fgsea" version))
3371 "0pbq3g515kcbi4wvfx8m09p01h2f8vwsi1qqsyahxz4r1fasz4c1"))))
3372 (build-system r-build-system)
3375 ("r-biocparallel" ,r-biocparallel)
3376 ("r-data-table" ,r-data-table)
3377 ("r-fastmatch" ,r-fastmatch)
3378 ("r-ggplot2" ,r-ggplot2)
3379 ("r-gridextra" ,r-gridextra)
3380 ("r-matrix" ,r-matrix)
3381 ("r-rcpp" ,r-rcpp)))
3382 (home-page "https://github.com/ctlab/fgsea/")
3383 (synopsis "Fast gene set enrichment analysis")
3385 "The package implements an algorithm for fast gene set enrichment
3386 analysis. Using the fast algorithm allows to make more permutations and get
3387 more fine grained p-values, which allows to use accurate stantard approaches
3388 to multiple hypothesis correction.")
3389 (license license:expat)))
3391 (define-public r-dose
3398 (uri (bioconductor-uri "DOSE" version))
3401 "0ss8mr28q0vswxjmhcas0aqag5nl099jbyn5w3ypbbxqwfvf9jj5"))))
3402 (properties `((upstream-name . "DOSE")))
3403 (build-system r-build-system)
3405 `(("r-annotationdbi" ,r-annotationdbi)
3406 ("r-biocparallel" ,r-biocparallel)
3407 ("r-do-db" ,r-do-db)
3408 ("r-fgsea" ,r-fgsea)
3409 ("r-ggplot2" ,r-ggplot2)
3410 ("r-gosemsim" ,r-gosemsim)
3411 ("r-qvalue" ,r-qvalue)
3412 ("r-reshape2" ,r-reshape2)
3413 ("r-s4vectors" ,r-s4vectors)))
3414 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3415 (synopsis "Disease ontology semantic and enrichment analysis")
3417 "This package implements five methods proposed by Resnik, Schlicker,
3418 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3419 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3420 including hypergeometric model and gene set enrichment analysis are also
3421 implemented for discovering disease associations of high-throughput biological
3423 (license license:artistic2.0)))
3425 (define-public r-enrichplot
3427 (name "r-enrichplot")
3432 (uri (bioconductor-uri "enrichplot" version))
3435 "0707f5ll58psh7pr001cmmk5di7dprnbry1cy2mw20vn8p24nf3x"))))
3436 (build-system r-build-system)
3438 `(("r-annotationdbi" ,r-annotationdbi)
3439 ("r-cowplot" ,r-cowplot)
3441 ("r-europepmc" ,r-europepmc)
3442 ("r-ggplot2" ,r-ggplot2)
3443 ("r-ggplotify" ,r-ggplotify)
3444 ("r-ggraph" ,r-ggraph)
3445 ("r-ggridges" ,r-ggridges)
3446 ("r-gosemsim" ,r-gosemsim)
3447 ("r-gridextra" ,r-gridextra)
3448 ("r-igraph" ,r-igraph)
3449 ("r-purrr" ,r-purrr)
3450 ("r-rcolorbrewer" ,r-rcolorbrewer)
3451 ("r-reshape2" ,r-reshape2)))
3452 (home-page "https://github.com/GuangchuangYu/enrichplot")
3453 (synopsis "Visualization of functional enrichment result")
3455 "The enrichplot package implements several visualization methods for
3456 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3457 All the visualization methods are developed based on ggplot2 graphics.")
3458 (license license:artistic2.0)))
3460 (define-public r-clusterprofiler
3462 (name "r-clusterprofiler")
3467 (uri (bioconductor-uri "clusterProfiler" version))
3470 "08pd7bmqmyxncj09ilz8yb9sf1pv9ni98y8b93pz2giy7pl407hg"))))
3472 `((upstream-name . "clusterProfiler")))
3473 (build-system r-build-system)
3475 `(("r-annotationdbi" ,r-annotationdbi)
3477 ("r-enrichplot" ,r-enrichplot)
3478 ("r-ggplot2" ,r-ggplot2)
3479 ("r-go-db" ,r-go-db)
3480 ("r-gosemsim" ,r-gosemsim)
3481 ("r-magrittr" ,r-magrittr)
3483 ("r-qvalue" ,r-qvalue)
3484 ("r-rvcheck" ,r-rvcheck)
3485 ("r-tidyr" ,r-tidyr)))
3486 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3487 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3489 "This package implements methods to analyze and visualize functional
3490 profiles (GO and KEGG) of gene and gene clusters.")
3491 (license license:artistic2.0)))
3493 (define-public r-mlinterfaces
3495 (name "r-mlinterfaces")
3500 (uri (bioconductor-uri "MLInterfaces" version))
3503 "1wc280iw9vllg6f58vsdj895yaqs8w42kl7jk8sgii009gwlaj8d"))))
3504 (properties `((upstream-name . "MLInterfaces")))
3505 (build-system r-build-system)
3507 `(("r-annotate" ,r-annotate)
3508 ("r-biobase" ,r-biobase)
3509 ("r-biocgenerics" ,r-biocgenerics)
3510 ("r-cluster" ,r-cluster)
3513 ("r-gdata" ,r-gdata)
3514 ("r-genefilter" ,r-genefilter)
3515 ("r-ggvis" ,r-ggvis)
3516 ("r-hwriter" ,r-hwriter)
3518 ("r-mlbench" ,r-mlbench)
3520 ("r-rcolorbrewer" ,r-rcolorbrewer)
3521 ("r-rpart" ,r-rpart)
3522 ("r-sfsmisc" ,r-sfsmisc)
3523 ("r-shiny" ,r-shiny)
3524 ("r-threejs" ,r-threejs)))
3525 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3526 (synopsis "Interfaces to R machine learning procedures")
3528 "This package provides uniform interfaces to machine learning code for
3529 data in R and Bioconductor containers.")
3530 ;; Any version of the LGPL.
3531 (license license:lgpl2.1+)))
3533 (define-public r-annaffy
3540 (uri (bioconductor-uri "annaffy" version))
3543 "1jrf4bq2wky4ay1jrcy60si6hxdcn4j05w5vgs38yfb92gq77i16"))))
3544 (build-system r-build-system)
3547 (modify-phases %standard-phases
3548 (add-after 'unpack 'remove-reference-to-non-free-data
3550 (substitute* "DESCRIPTION"
3554 `(("r-annotationdbi" ,r-annotationdbi)
3555 ("r-biobase" ,r-biobase)
3557 ("r-go-db" ,r-go-db)))
3558 (home-page "https://bioconductor.org/packages/annaffy/")
3559 (synopsis "Annotation tools for Affymetrix biological metadata")
3561 "This package provides functions for handling data from Bioconductor
3562 Affymetrix annotation data packages. It produces compact HTML and text
3563 reports including experimental data and URL links to many online databases.
3564 It allows searching of biological metadata using various criteria.")
3565 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3566 ;; the LGPL 2.1 is included.
3567 (license license:lgpl2.1+)))
3569 (define-public r-a4core
3576 (uri (bioconductor-uri "a4Core" version))
3579 "0xcs9wl2yrprl4yc0z5s4zrkil3752k9xc1fi8fcx7zab1mm80df"))))
3580 (properties `((upstream-name . "a4Core")))
3581 (build-system r-build-system)
3583 `(("r-biobase" ,r-biobase)
3584 ("r-glmnet" ,r-glmnet)))
3585 (home-page "https://bioconductor.org/packages/a4Core")
3586 (synopsis "Automated Affymetrix array analysis core package")
3588 "This is the core package for the automated analysis of Affymetrix
3590 (license license:gpl3)))
3592 (define-public r-a4classif
3594 (name "r-a4classif")
3599 (uri (bioconductor-uri "a4Classif" version))
3602 "0gj3hdflfs1ybc2kshl9w1dzy0rfzppfj08hx3wa2chjsm0m9brn"))))
3603 (properties `((upstream-name . "a4Classif")))
3604 (build-system r-build-system)
3606 `(("r-a4core" ,r-a4core)
3607 ("r-a4preproc" ,r-a4preproc)
3608 ("r-glmnet" ,r-glmnet)
3609 ("r-mlinterfaces" ,r-mlinterfaces)
3612 ("r-varselrf" ,r-varselrf)))
3613 (home-page "https://bioconductor.org/packages/a4Classif/")
3614 (synopsis "Automated Affymetrix array analysis classification package")
3616 "This is the classification package for the automated analysis of
3617 Affymetrix arrays.")
3618 (license license:gpl3)))
3620 (define-public r-a4preproc
3622 (name "r-a4preproc")
3627 (uri (bioconductor-uri "a4Preproc" version))
3630 "11j5nc33gd6yis1fyagr0y39g21bzkc59kq8b8sd6b3pfc84zrjd"))))
3631 (properties `((upstream-name . "a4Preproc")))
3632 (build-system r-build-system)
3634 `(("r-annotationdbi" ,r-annotationdbi)))
3635 (home-page "https://bioconductor.org/packages/a4Preproc/")
3636 (synopsis "Automated Affymetrix array analysis preprocessing package")
3638 "This is a package for the automated analysis of Affymetrix arrays. It
3639 is used for preprocessing the arrays.")
3640 (license license:gpl3)))
3642 (define-public r-a4reporting
3644 (name "r-a4reporting")
3649 (uri (bioconductor-uri "a4Reporting" version))
3652 "15nd4pa5hkdzkhinvqw5ijdqb7k5gk37v2hmk3jsg2d6m0jqphi5"))))
3653 (properties `((upstream-name . "a4Reporting")))
3654 (build-system r-build-system)
3656 `(("r-annaffy" ,r-annaffy)
3657 ("r-xtable" ,r-xtable)))
3658 (home-page "https://bioconductor.org/packages/a4Reporting/")
3659 (synopsis "Automated Affymetrix array analysis reporting package")
3661 "This is a package for the automated analysis of Affymetrix arrays. It
3662 provides reporting features.")
3663 (license license:gpl3)))
3665 (define-public r-a4base
3672 (uri (bioconductor-uri "a4Base" version))
3675 "0dgqyq4dnlcik5qqygnhxlhfr98sh6kmdcj2qllhrwyk0lmsfk01"))))
3676 (properties `((upstream-name . "a4Base")))
3677 (build-system r-build-system)
3679 `(("r-a4core" ,r-a4core)
3680 ("r-a4preproc" ,r-a4preproc)
3681 ("r-annaffy" ,r-annaffy)
3682 ("r-annotationdbi" ,r-annotationdbi)
3683 ("r-biobase" ,r-biobase)
3684 ("r-genefilter" ,r-genefilter)
3685 ("r-glmnet" ,r-glmnet)
3686 ("r-gplots" ,r-gplots)
3687 ("r-limma" ,r-limma)
3689 ("r-multtest" ,r-multtest)))
3690 (home-page "https://bioconductor.org/packages/a4Base/")
3691 (synopsis "Automated Affymetrix array analysis base package")
3693 "This package provides basic features for the automated analysis of
3694 Affymetrix arrays.")
3695 (license license:gpl3)))
3704 (uri (bioconductor-uri "a4" version))
3707 "14yipy6s2wqr9q0yp09x1mm17npknrhs6yd34i3wrb5id64ywnq4"))))
3708 (build-system r-build-system)
3710 `(("r-a4base" ,r-a4base)
3711 ("r-a4classif" ,r-a4classif)
3712 ("r-a4core" ,r-a4core)
3713 ("r-a4preproc" ,r-a4preproc)
3714 ("r-a4reporting" ,r-a4reporting)))
3715 (home-page "https://bioconductor.org/packages/a4/")
3716 (synopsis "Automated Affymetrix array analysis umbrella package")
3718 "This package provides a software suite for the automated analysis of
3719 Affymetrix arrays.")
3720 (license license:gpl3)))
3722 (define-public r-abseqr
3729 (uri (bioconductor-uri "abseqR" version))
3732 "1n9h5qkj4njr1f8fvhg9sj9wxcd7hljnnk8m80zwswzs2n9ivppa"))))
3733 (properties `((upstream-name . "abseqR")))
3734 (build-system r-build-system)
3736 `(("pandoc" ,ghc-pandoc)))
3738 `(("r-biocparallel" ,r-biocparallel)
3739 ("r-biocstyle" ,r-biocstyle)
3740 ("r-circlize" ,r-circlize)
3741 ("r-flexdashboard" ,r-flexdashboard)
3742 ("r-ggcorrplot" ,r-ggcorrplot)
3743 ("r-ggdendro" ,r-ggdendro)
3744 ("r-ggplot2" ,r-ggplot2)
3745 ("r-gridextra" ,r-gridextra)
3746 ("r-knitr" ,r-knitr)
3747 ("r-plotly" ,r-plotly)
3750 ("r-rcolorbrewer" ,r-rcolorbrewer)
3751 ("r-reshape2" ,r-reshape2)
3752 ("r-rmarkdown" ,r-rmarkdown)
3753 ("r-stringr" ,r-stringr)
3754 ("r-vegan" ,r-vegan)
3755 ("r-venndiagram" ,r-venndiagram)))
3756 (home-page "https://github.com/malhamdoosh/abseqR")
3757 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3759 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3760 sequencing datasets generated from antibody libraries and abseqR is one of its
3761 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3762 capabilities and allows them to generate interactive HTML reports for the
3763 convenience of viewing and sharing with other researchers. Additionally,
3764 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3765 further downstream analysis on its output.")
3766 (license license:gpl3)))
3768 (define-public r-bacon
3775 (uri (bioconductor-uri "bacon" version))
3778 "1q18vm4znl47v56cnvx9y5ygrial2mdjpl8x1043jq00kyygrc86"))))
3779 (build-system r-build-system)
3781 `(("r-biocparallel" ,r-biocparallel)
3782 ("r-ellipse" ,r-ellipse)
3783 ("r-ggplot2" ,r-ggplot2)))
3784 (home-page "https://bioconductor.org/packages/bacon/")
3785 (synopsis "Controlling bias and inflation in association studies")
3787 "Bacon can be used to remove inflation and bias often observed in
3788 epigenome- and transcriptome-wide association studies. To this end bacon
3789 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3790 fitting a three-component normal mixture on z-scores.")
3791 (license license:gpl2+)))
3793 (define-public r-rgadem
3800 (uri (bioconductor-uri "rGADEM" version))
3803 "12xm4p4qsczf57kip8bvi6pr8sb5gvn11dnbz7lbh6sc03sx3q2h"))))
3804 (properties `((upstream-name . "rGADEM")))
3805 (build-system r-build-system)
3807 `(("r-biostrings" ,r-biostrings)
3808 ("r-bsgenome" ,r-bsgenome)
3809 ("r-genomicranges" ,r-genomicranges)
3810 ("r-iranges" ,r-iranges)
3811 ("r-seqlogo" ,r-seqlogo)))
3812 (home-page "https://bioconductor.org/packages/rGADEM/")
3813 (synopsis "De novo sequence motif discovery")
3815 "rGADEM is an efficient de novo motif discovery tool for large-scale
3816 genomic sequence data.")
3817 (license license:artistic2.0)))
3819 (define-public r-motiv
3826 (uri (bioconductor-uri "MotIV" version))
3829 "07k4rw4nhcn4sg43psv1h7qr064gws22m2yyr7x8sy3f1i1c954k"))))
3830 (properties `((upstream-name . "MotIV")))
3831 (build-system r-build-system)
3835 `(("r-biocgenerics" ,r-biocgenerics)
3836 ("r-biostrings" ,r-biostrings)
3837 ("r-genomicranges" ,r-genomicranges)
3838 ("r-iranges" ,r-iranges)
3839 ("r-lattice" ,r-lattice)
3840 ("r-rgadem" ,r-rgadem)
3841 ("r-s4vectors" ,r-s4vectors)))
3842 (home-page "https://bioconductor.org/packages/MotIV/")
3843 (synopsis "Motif identification and validation")
3845 "This package is used for the identification and validation of sequence
3846 motifs. It makes use of STAMP for comparing a set of motifs to a given
3847 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3848 distributions, modules and filter motifs.")
3849 (license license:gpl2)))
3851 (define-public r-motifstack
3853 (name "r-motifstack")
3858 (uri (bioconductor-uri "motifStack" version))
3861 "00rafqs1gqlcxlbsdn9qnq9xb7wjphiksb3hsx76viqjbjzi14wg"))))
3862 (properties `((upstream-name . "motifStack")))
3863 (build-system r-build-system)
3865 `(("r-ade4" ,r-ade4)
3866 ("r-biostrings" ,r-biostrings)
3867 ("r-ggplot2" ,r-ggplot2)
3868 ("r-grimport2" ,r-grimport2)
3869 ("r-htmlwidgets" ,r-htmlwidgets)
3870 ("r-motiv" ,r-motiv)
3871 ("r-scales" ,r-scales)
3873 (home-page "https://bioconductor.org/packages/motifStack/")
3874 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3876 "The motifStack package is designed for graphic representation of
3877 multiple motifs with different similarity scores. It works with both DNA/RNA
3878 sequence motifs and amino acid sequence motifs. In addition, it provides the
3879 flexibility for users to customize the graphic parameters such as the font
3880 type and symbol colors.")
3881 (license license:gpl2+)))
3883 (define-public r-genomicscores
3885 (name "r-genomicscores")
3890 (uri (bioconductor-uri "GenomicScores" version))
3893 "175iaqv7npa11yw48vmqpgx0qqs3g44c3dsya7ccwd1lg97fznkj"))))
3894 (properties `((upstream-name . "GenomicScores")))
3895 (build-system r-build-system)
3897 `(("r-annotationhub" ,r-annotationhub)
3898 ("r-biobase" ,r-biobase)
3899 ("r-biocgenerics" ,r-biocgenerics)
3900 ("r-biostrings" ,r-biostrings)
3901 ("r-bsgenome" ,r-bsgenome)
3902 ("r-genomeinfodb" ,r-genomeinfodb)
3903 ("r-genomicranges" ,r-genomicranges)
3904 ("r-iranges" ,r-iranges)
3905 ("r-s4vectors" ,r-s4vectors)
3907 (home-page "https://github.com/rcastelo/GenomicScores/")
3908 (synopsis "Work with genome-wide position-specific scores")
3910 "This package provides infrastructure to store and access genome-wide
3911 position-specific scores within R and Bioconductor.")
3912 (license license:artistic2.0)))
3914 (define-public r-atacseqqc
3916 (name "r-atacseqqc")
3921 (uri (bioconductor-uri "ATACseqQC" version))
3924 "12ix0bvwk50d48z85f3453k7szm1j27gk4qgw56az4fxra472rlh"))))
3925 (properties `((upstream-name . "ATACseqQC")))
3926 (build-system r-build-system)
3928 `(("r-biocgenerics" ,r-biocgenerics)
3929 ("r-biostrings" ,r-biostrings)
3930 ("r-bsgenome" ,r-bsgenome)
3931 ("r-chippeakanno" ,r-chippeakanno)
3932 ("r-edger" ,r-edger)
3933 ("r-genomeinfodb" ,r-genomeinfodb)
3934 ("r-genomicalignments" ,r-genomicalignments)
3935 ("r-genomicranges" ,r-genomicranges)
3936 ("r-genomicscores" ,r-genomicscores)
3937 ("r-iranges" ,r-iranges)
3938 ("r-kernsmooth" ,r-kernsmooth)
3939 ("r-limma" ,r-limma)
3940 ("r-motifstack" ,r-motifstack)
3941 ("r-preseqr" ,r-preseqr)
3942 ("r-randomforest" ,r-randomforest)
3943 ("r-rsamtools" ,r-rsamtools)
3944 ("r-rtracklayer" ,r-rtracklayer)
3945 ("r-s4vectors" ,r-s4vectors)))
3946 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3947 (synopsis "ATAC-seq quality control")
3949 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3950 sequencing, is a rapid and sensitive method for chromatin accessibility
3951 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3952 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3953 assess whether their ATAC-seq experiment is successful. It includes
3954 diagnostic plots of fragment size distribution, proportion of mitochondria
3955 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3957 (license license:gpl2+)))
3959 (define-public r-gofuncr
3966 (uri (bioconductor-uri "GOfuncR" version))
3969 "0hmi13pz923fm95asys615rih63b1i2nvynfczr1zcsc9fzn4h35"))))
3970 (properties `((upstream-name . "GOfuncR")))
3971 (build-system r-build-system)
3973 `(("r-annotationdbi" ,r-annotationdbi)
3974 ("r-genomicranges" ,r-genomicranges)
3975 ("r-gtools" ,r-gtools)
3976 ("r-iranges" ,r-iranges)
3977 ("r-mapplots" ,r-mapplots)
3979 ("r-vioplot" ,r-vioplot)))
3980 (home-page "https://bioconductor.org/packages/GOfuncR/")
3981 (synopsis "Gene ontology enrichment using FUNC")
3983 "GOfuncR performs a gene ontology enrichment analysis based on the
3984 ontology enrichment software FUNC. GO-annotations are obtained from
3985 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3986 included in the package and updated regularly. GOfuncR provides the standard
3987 candidate vs background enrichment analysis using the hypergeometric test, as
3988 well as three additional tests:
3991 @item the Wilcoxon rank-sum test that is used when genes are ranked,
3992 @item a binomial test that is used when genes are associated with two counts,
3994 @item a Chi-square or Fisher's exact test that is used in cases when genes are
3995 associated with four counts.
3998 To correct for multiple testing and interdependency of the tests, family-wise
3999 error rates are computed based on random permutations of the gene-associated
4000 variables. GOfuncR also provides tools for exploring the ontology graph and
4001 the annotations, and options to take gene-length or spatial clustering of
4002 genes into account. It is also possible to provide custom gene coordinates,
4003 annotations and ontologies.")
4004 (license license:gpl2+)))
4006 (define-public r-abaenrichment
4008 (name "r-abaenrichment")
4013 (uri (bioconductor-uri "ABAEnrichment" version))
4016 "128ik28j8kmdkycffhxajv5h174zdq9sfn2gz6ai90wgkdadbzwp"))))
4017 (properties `((upstream-name . "ABAEnrichment")))
4018 (build-system r-build-system)
4020 `(("r-abadata" ,r-abadata)
4021 ("r-data-table" ,r-data-table)
4022 ("r-gofuncr" ,r-gofuncr)
4023 ("r-gplots" ,r-gplots)
4024 ("r-gtools" ,r-gtools)
4025 ("r-rcpp" ,r-rcpp)))
4026 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4027 (synopsis "Gene expression enrichment in human brain regions")
4029 "The package ABAEnrichment is designed to test for enrichment of user
4030 defined candidate genes in the set of expressed genes in different human brain
4031 regions. The core function @code{aba_enrich} integrates the expression of the
4032 candidate gene set (averaged across donors) and the structural information of
4033 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4034 (license license:gpl2+)))
4036 (define-public r-annotationfuncs
4038 (name "r-annotationfuncs")
4043 (uri (bioconductor-uri "AnnotationFuncs" version))
4046 "0ws14b1ibqml7w8kj0gi7wdp6wd8dcdpnrmcxldjzsyawf17q0yq"))))
4048 `((upstream-name . "AnnotationFuncs")))
4049 (build-system r-build-system)
4051 `(("r-annotationdbi" ,r-annotationdbi)
4053 (home-page "https://www.iysik.com/r/annotationfuncs")
4054 (synopsis "Annotation translation functions")
4056 "This package provides functions for handling translating between
4057 different identifieres using the Biocore Data Team data-packages (e.g.
4058 @code{org.Bt.eg.db}).")
4059 (license license:gpl2)))
4061 (define-public r-annotationtools
4063 (name "r-annotationtools")
4068 (uri (bioconductor-uri "annotationTools" version))
4071 "1cq7ayq2swp2ahlphz74nh5mb869rgyyr0kkqy1mxyilk8k2g44i"))))
4073 `((upstream-name . "annotationTools")))
4074 (build-system r-build-system)
4075 (propagated-inputs `(("r-biobase" ,r-biobase)))
4076 (home-page "https://bioconductor.org/packages/annotationTools/")
4077 (synopsis "Annotate microarrays and perform gene expression analyses")
4079 "This package provides functions to annotate microarrays, find orthologs,
4080 and integrate heterogeneous gene expression profiles using annotation and
4081 other molecular biology information available as flat file database (plain
4083 ;; Any version of the GPL.
4084 (license (list license:gpl2+))))
4086 (define-public r-allelicimbalance
4088 (name "r-allelicimbalance")
4093 (uri (bioconductor-uri "AllelicImbalance" version))
4096 "0vy8w7ii2qljsmq8lr21lygkcrsshc7syyqhadlbxyj3scgi7kyc"))))
4098 `((upstream-name . "AllelicImbalance")))
4099 (build-system r-build-system)
4101 `(("r-annotationdbi" ,r-annotationdbi)
4102 ("r-biocgenerics" ,r-biocgenerics)
4103 ("r-biostrings" ,r-biostrings)
4104 ("r-bsgenome" ,r-bsgenome)
4105 ("r-genomeinfodb" ,r-genomeinfodb)
4106 ("r-genomicalignments" ,r-genomicalignments)
4107 ("r-genomicfeatures" ,r-genomicfeatures)
4108 ("r-genomicranges" ,r-genomicranges)
4109 ("r-gridextra" ,r-gridextra)
4111 ("r-iranges" ,r-iranges)
4112 ("r-lattice" ,r-lattice)
4113 ("r-latticeextra" ,r-latticeextra)
4115 ("r-rsamtools" ,r-rsamtools)
4116 ("r-s4vectors" ,r-s4vectors)
4117 ("r-seqinr" ,r-seqinr)
4118 ("r-summarizedexperiment" ,r-summarizedexperiment)
4119 ("r-variantannotation" ,r-variantannotation)))
4120 (home-page "https://github.com/pappewaio/AllelicImbalance")
4121 (synopsis "Investigate allele-specific expression")
4123 "This package provides a framework for allele-specific expression
4124 investigation using RNA-seq data.")
4125 (license license:gpl3)))
4127 (define-public r-aucell
4134 (uri (bioconductor-uri "AUCell" version))
4137 "1g4mdq8z29fjxrfjng0fb3cvbph49mwds4ijsa2bn2k6f75dnzky"))))
4138 (properties `((upstream-name . "AUCell")))
4139 (build-system r-build-system)
4141 `(("r-biocgenerics" ,r-biocgenerics)
4142 ("r-data-table" ,r-data-table)
4143 ("r-gseabase" ,r-gseabase)
4144 ("r-mixtools" ,r-mixtools)
4145 ("r-r-utils" ,r-r-utils)
4146 ("r-s4vectors" ,r-s4vectors)
4147 ("r-shiny" ,r-shiny)
4148 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4149 (home-page "https://bioconductor.org/packages/AUCell/")
4150 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4152 "AUCell allows to identify cells with active gene sets (e.g. signatures,
4153 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4154 Under the Curve} (AUC) to calculate whether a critical subset of the input
4155 gene set is enriched within the expressed genes for each cell. The
4156 distribution of AUC scores across all the cells allows exploring the relative
4157 expression of the signature. Since the scoring method is ranking-based,
4158 AUCell is independent of the gene expression units and the normalization
4159 procedure. In addition, since the cells are evaluated individually, it can
4160 easily be applied to bigger datasets, subsetting the expression matrix if
4162 (license license:gpl3)))
4164 (define-public r-ebimage
4171 (uri (bioconductor-uri "EBImage" version))
4174 "0q54q2nw6p1s4nrj1l8qz78m67xcysj2x82zs43my8iv2g9iifgs"))))
4175 (properties `((upstream-name . "EBImage")))
4176 (build-system r-build-system)
4178 `(("r-abind" ,r-abind)
4179 ("r-biocgenerics" ,r-biocgenerics)
4180 ("r-fftwtools" ,r-fftwtools)
4181 ("r-htmltools" ,r-htmltools)
4182 ("r-htmlwidgets" ,r-htmlwidgets)
4184 ("r-locfit" ,r-locfit)
4186 ("r-rcurl" ,r-rcurl)
4187 ("r-tiff" ,r-tiff)))
4189 `(("r-knitr" ,r-knitr))) ; for vignettes
4190 (home-page "https://github.com/aoles/EBImage")
4191 (synopsis "Image processing and analysis toolbox for R")
4193 "EBImage provides general purpose functionality for image processing and
4194 analysis. In the context of (high-throughput) microscopy-based cellular
4195 assays, EBImage offers tools to segment cells and extract quantitative
4196 cellular descriptors. This allows the automation of such tasks using the R
4197 programming language and facilitates the use of other tools in the R
4198 environment for signal processing, statistical modeling, machine learning and
4199 visualization with image data.")
4200 ;; Any version of the LGPL.
4201 (license license:lgpl2.1+)))
4203 (define-public r-yamss
4210 (uri (bioconductor-uri "yamss" version))
4213 "1n49a2vg1667wycrjww29xfafngllvpb5nq5wy6pgn0akva91nky"))))
4214 (build-system r-build-system)
4216 `(("r-biocgenerics" ,r-biocgenerics)
4217 ("r-data-table" ,r-data-table)
4218 ("r-ebimage" ,r-ebimage)
4219 ("r-iranges" ,r-iranges)
4220 ("r-limma" ,r-limma)
4221 ("r-matrix" ,r-matrix)
4223 ("r-s4vectors" ,r-s4vectors)
4224 ("r-summarizedexperiment"
4225 ,r-summarizedexperiment)))
4226 (home-page "https://github.com/hansenlab/yamss")
4227 (synopsis "Tools for high-throughput metabolomics")
4229 "This package provides tools to analyze and visualize high-throughput
4230 metabolomics data acquired using chromatography-mass spectrometry. These tools
4231 preprocess data in a way that enables reliable and powerful differential
4233 (license license:artistic2.0)))
4235 (define-public r-gtrellis
4242 (uri (bioconductor-uri "gtrellis" version))
4245 "0mgspmv6p1a2k98jyy2dfl0wpa2vh7bhnjfm2xaqmcsxzmbjhh9z"))))
4246 (build-system r-build-system)
4248 `(("r-circlize" ,r-circlize)
4249 ("r-genomicranges" ,r-genomicranges)
4250 ("r-getoptlong" ,r-getoptlong)
4251 ("r-iranges" ,r-iranges)))
4252 (home-page "https://github.com/jokergoo/gtrellis")
4253 (synopsis "Genome level Trellis layout")
4255 "Genome level Trellis graph visualizes genomic data conditioned by
4256 genomic categories (e.g. chromosomes). For each genomic category, multiple
4257 dimensional data which are represented as tracks describe different features
4258 from different aspects. This package provides high flexibility to arrange
4259 genomic categories and to add self-defined graphics in the plot.")
4260 (license license:expat)))
4262 (define-public r-somaticsignatures
4264 (name "r-somaticsignatures")
4269 (uri (bioconductor-uri "SomaticSignatures" version))
4272 "1gvrkahllwz38g3hn9pjlikhfqz19a4qglcqmyrxk7h9ybx5zy5z"))))
4274 `((upstream-name . "SomaticSignatures")))
4275 (build-system r-build-system)
4277 `(("r-biobase" ,r-biobase)
4278 ("r-biostrings" ,r-biostrings)
4279 ("r-genomeinfodb" ,r-genomeinfodb)
4280 ("r-genomicranges" ,r-genomicranges)
4281 ("r-ggbio" ,r-ggbio)
4282 ("r-ggplot2" ,r-ggplot2)
4283 ("r-iranges" ,r-iranges)
4285 ("r-pcamethods" ,r-pcamethods)
4286 ("r-proxy" ,r-proxy)
4287 ("r-reshape2" ,r-reshape2)
4288 ("r-s4vectors" ,r-s4vectors)
4289 ("r-variantannotation" ,r-variantannotation)))
4290 (home-page "https://github.com/juliangehring/SomaticSignatures")
4291 (synopsis "Somatic signatures")
4293 "This package identifies mutational signatures of @dfn{single nucleotide
4294 variants} (SNVs). It provides a infrastructure related to the methodology
4295 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4296 decomposition algorithms.")
4297 (license license:expat)))
4299 (define-public r-yapsa
4306 (uri (bioconductor-uri "YAPSA" version))
4309 "132x51f8k8zyx6j8jk05x4lr9q1hlblgvr69wkhn0q3f8mhaj926"))))
4310 (properties `((upstream-name . "YAPSA")))
4311 (build-system r-build-system)
4313 `(("r-circlize" ,r-circlize)
4314 ("r-complexheatmap" ,r-complexheatmap)
4315 ("r-corrplot" ,r-corrplot)
4316 ("r-dendextend" ,r-dendextend)
4317 ("r-genomeinfodb" ,r-genomeinfodb)
4318 ("r-genomicranges" ,r-genomicranges)
4319 ("r-getoptlong" ,r-getoptlong)
4320 ("r-ggplot2" ,r-ggplot2)
4321 ("r-gridextra" ,r-gridextra)
4322 ("r-gtrellis" ,r-gtrellis)
4323 ("r-keggrest" ,r-keggrest)
4325 ("r-pmcmr" ,r-pmcmr)
4326 ("r-reshape2" ,r-reshape2)
4327 ("r-somaticsignatures" ,r-somaticsignatures)
4328 ("r-variantannotation" ,r-variantannotation)))
4329 (home-page "https://bioconductor.org/packages/YAPSA/")
4330 (synopsis "Yet another package for signature analysis")
4332 "This package provides functions and routines useful in the analysis of
4333 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4334 functions to perform a signature analysis with known signatures and a
4335 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4337 (license license:gpl3)))
4339 (define-public r-gcrma
4346 (uri (bioconductor-uri "gcrma" version))
4349 "0c9sa9ldlcpdcjdan8m4ndnyaisr6wbarq486sl44ikh7wf1csfx"))))
4350 (build-system r-build-system)
4352 `(("r-affy" ,r-affy)
4353 ("r-affyio" ,r-affyio)
4354 ("r-biobase" ,r-biobase)
4355 ("r-biocmanager" ,r-biocmanager)
4356 ("r-biostrings" ,r-biostrings)
4357 ("r-xvector" ,r-xvector)))
4358 (home-page "https://bioconductor.org/packages/gcrma/")
4359 (synopsis "Background adjustment using sequence information")
4361 "Gcrma adjusts for background intensities in Affymetrix array data which
4362 include optical noise and @dfn{non-specific binding} (NSB). The main function
4363 @code{gcrma} converts background adjusted probe intensities to expression
4364 measures using the same normalization and summarization methods as a
4365 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4366 to estimate probe affinity to NSB. The sequence information is summarized in
4367 a more complex way than the simple GC content. Instead, the base types (A, T,
4368 G or C) at each position along the probe determine the affinity of each probe.
4369 The parameters of the position-specific base contributions to the probe
4370 affinity is estimated in an NSB experiment in which only NSB but no
4371 gene-specific bidning is expected.")
4372 ;; Any version of the LGPL
4373 (license license:lgpl2.1+)))
4375 (define-public r-simpleaffy
4377 (name "r-simpleaffy")
4382 (uri (bioconductor-uri "simpleaffy" version))
4385 "18bz3pfgp0f7906flrljx97ann8s71pnb8gpw7nah46n8vqc0xcs"))))
4386 (build-system r-build-system)
4388 `(("r-affy" ,r-affy)
4389 ("r-biobase" ,r-biobase)
4390 ("r-biocgenerics" ,r-biocgenerics)
4391 ("r-gcrma" ,r-gcrma)
4392 ("r-genefilter" ,r-genefilter)))
4393 (home-page "https://bioconductor.org/packages/simpleaffy/")
4394 (synopsis "Very simple high level analysis of Affymetrix data")
4396 "This package provides high level functions for reading Affy @file{.CEL}
4397 files, phenotypic data, and then computing simple things with it, such as
4398 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4399 library. It also has some basic scatter plot functions and mechanisms for
4400 generating high resolution journal figures.")
4401 (license license:gpl2+)))
4403 (define-public r-yaqcaffy
4410 (uri (bioconductor-uri "yaqcaffy" version))
4413 "0kzzqsf1lfbcmy95w2z0c9qrvp7mbwm50k2l9wvz3xa5wz6xa7gz"))))
4414 (build-system r-build-system)
4416 `(("r-simpleaffy" ,r-simpleaffy)))
4417 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4418 (synopsis "Affymetrix quality control and reproducibility analysis")
4420 "This is a package that can be used for quality control of Affymetrix
4421 GeneChip expression data and reproducibility analysis of human whole genome
4422 chips with the MAQC reference datasets.")
4423 (license license:artistic2.0)))
4425 (define-public r-quantro
4432 (uri (bioconductor-uri "quantro" version))
4435 "09f3x1j50ll5hhn3qwys5x06mii3fqsrk6dkvsxai0kdxv9cjz9m"))))
4436 (build-system r-build-system)
4438 `(("r-biobase" ,r-biobase)
4439 ("r-doparallel" ,r-doparallel)
4440 ("r-foreach" ,r-foreach)
4441 ("r-ggplot2" ,r-ggplot2)
4442 ("r-iterators" ,r-iterators)
4443 ("r-minfi" ,r-minfi)
4444 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4445 (home-page "https://bioconductor.org/packages/quantro/")
4446 (synopsis "Test for when to use quantile normalization")
4448 "This package provides a data-driven test for the assumptions of quantile
4449 normalization using raw data such as objects that inherit eSets (e.g.
4450 ExpressionSet, MethylSet). Group level information about each sample (such as
4451 Tumor / Normal status) must also be provided because the test assesses if
4452 there are global differences in the distributions between the user-defined
4454 (license license:gpl3+)))
4456 (define-public r-yarn
4463 (uri (bioconductor-uri "yarn" version))
4466 "0891a10adkhm1zpm7fpcxc2xfxjf9yrpckaz87b2wdjdiwivc4cp"))))
4467 (build-system r-build-system)
4469 `(("r-biobase" ,r-biobase)
4470 ("r-biomart" ,r-biomart)
4471 ("r-downloader" ,r-downloader)
4472 ("r-edger" ,r-edger)
4473 ("r-gplots" ,r-gplots)
4474 ("r-limma" ,r-limma)
4475 ("r-matrixstats" ,r-matrixstats)
4476 ("r-preprocesscore" ,r-preprocesscore)
4477 ("r-quantro" ,r-quantro)
4478 ("r-rcolorbrewer" ,r-rcolorbrewer)
4479 ("r-readr" ,r-readr)))
4480 (home-page "https://bioconductor.org/packages/yarn/")
4481 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4483 "Expedite large RNA-Seq analyses using a combination of previously
4484 developed tools. YARN is meant to make it easier for the user in performing
4485 basic mis-annotation quality control, filtering, and condition-aware
4486 normalization. YARN leverages many Bioconductor tools and statistical
4487 techniques to account for the large heterogeneity and sparsity found in very
4488 large RNA-seq experiments.")
4489 (license license:artistic2.0)))
4491 (define-public r-roar
4498 (uri (bioconductor-uri "roar" version))
4501 "1nqw0agx9x8ycdf0gw17fdlnmzpw9x3zig1wcy10xpyhyjdbbi06"))))
4502 (build-system r-build-system)
4504 `(("r-biocgenerics" ,r-biocgenerics)
4505 ("r-genomeinfodb" ,r-genomeinfodb)
4506 ("r-genomicalignments" ,r-genomicalignments)
4507 ("r-genomicranges" ,r-genomicranges)
4508 ("r-iranges" ,r-iranges)
4509 ("r-rtracklayer" ,r-rtracklayer)
4510 ("r-s4vectors" ,r-s4vectors)
4511 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4512 (home-page "https://github.com/vodkatad/roar/")
4513 (synopsis "Identify differential APA usage from RNA-seq alignments")
4515 "This package provides tools for identifying preferential usage of APA
4516 sites, comparing two biological conditions, starting from known alternative
4517 sites and alignments obtained from standard RNA-seq experiments.")
4518 (license license:gpl3)))
4520 (define-public r-xbseq
4527 (uri (bioconductor-uri "XBSeq" version))
4530 "1qr5gvf8jcx6r0ac7d2wmnikswmp3k71lirnw7dyr6fndzrdz9lp"))))
4531 (properties `((upstream-name . "XBSeq")))
4532 (build-system r-build-system)
4534 `(("r-biobase" ,r-biobase)
4535 ("r-deseq2" ,r-deseq2)
4536 ("r-dplyr" ,r-dplyr)
4537 ("r-ggplot2" ,r-ggplot2)
4538 ("r-locfit" ,r-locfit)
4539 ("r-magrittr" ,r-magrittr)
4540 ("r-matrixstats" ,r-matrixstats)
4541 ("r-pracma" ,r-pracma)
4542 ("r-roar" ,r-roar)))
4543 (home-page "https://github.com/Liuy12/XBSeq")
4544 (synopsis "Test for differential expression for RNA-seq data")
4546 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4547 expression} (DE), where a statistical model was established based on the
4548 assumption that observed signals are the convolution of true expression
4549 signals and sequencing noises. The mapped reads in non-exonic regions are
4550 considered as sequencing noises, which follows a Poisson distribution. Given
4551 measurable observed signal and background noise from RNA-seq data, true
4552 expression signals, assuming governed by the negative binomial distribution,
4553 can be delineated and thus the accurate detection of differential expressed
4555 (license license:gpl3+)))
4557 (define-public r-massspecwavelet
4559 (name "r-massspecwavelet")
4564 (uri (bioconductor-uri "MassSpecWavelet" version))
4567 "0xnj3ncrwvr2b8msi3g77mgzj0zaksn3lgqdn1abh0ww5wgk83v7"))))
4569 `((upstream-name . "MassSpecWavelet")))
4570 (build-system r-build-system)
4572 `(("r-waveslim" ,r-waveslim)))
4573 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4574 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4576 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4577 data mainly through the use of wavelet transforms. It supports peak detection
4578 based on @dfn{Continuous Wavelet Transform} (CWT).")
4579 (license license:lgpl2.0+)))
4581 (define-public r-xcms
4588 (uri (bioconductor-uri "xcms" version))
4591 "18iglvlvlxrdwn2apdvihj9jxmx0kwm5z37rml67xcj9sfdi3bjb"))))
4592 (build-system r-build-system)
4594 `(("r-biobase" ,r-biobase)
4595 ("r-biocgenerics" ,r-biocgenerics)
4596 ("r-biocparallel" ,r-biocparallel)
4597 ("r-iranges" ,r-iranges)
4598 ("r-lattice" ,r-lattice)
4599 ("r-massspecwavelet" ,r-massspecwavelet)
4600 ("r-msnbase" ,r-msnbase)
4601 ("r-multtest" ,r-multtest)
4604 ("r-protgenerics" ,r-protgenerics)
4606 ("r-rcolorbrewer" ,r-rcolorbrewer)
4607 ("r-robustbase" ,r-robustbase)
4608 ("r-s4vectors" ,r-s4vectors)))
4609 (home-page "https://bioconductor.org/packages/xcms/")
4610 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4612 "This package provides a framework for processing and visualization of
4613 chromatographically separated and single-spectra mass spectral data. It
4614 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4615 data for high-throughput, untargeted analyte profiling.")
4616 (license license:gpl2+)))
4618 (define-public r-wrench
4625 (uri (bioconductor-uri "Wrench" version))
4628 "1s8d7jn0dk5zk2fhvsd4sgicypz4c41nzf19nqzcwb9bd6asgrwm"))))
4629 (properties `((upstream-name . "Wrench")))
4630 (build-system r-build-system)
4632 `(("r-limma" ,r-limma)
4633 ("r-locfit" ,r-locfit)
4634 ("r-matrixstats" ,r-matrixstats)))
4635 (home-page "https://github.com/HCBravoLab/Wrench")
4636 (synopsis "Wrench normalization for sparse count data")
4638 "Wrench is a package for normalization sparse genomic count data, like
4639 that arising from 16s metagenomic surveys.")
4640 (license license:artistic2.0)))
4642 (define-public r-wiggleplotr
4644 (name "r-wiggleplotr")
4649 (uri (bioconductor-uri "wiggleplotr" version))
4652 "1pj2bsn5azs18mp5hr4g7c6rnds2y2rjjnak2785kaj7xi8jly4m"))))
4653 (build-system r-build-system)
4655 `(("r-assertthat" ,r-assertthat)
4656 ("r-cowplot" ,r-cowplot)
4657 ("r-dplyr" ,r-dplyr)
4658 ("r-genomeinfodb" ,r-genomeinfodb)
4659 ("r-genomicranges" ,r-genomicranges)
4660 ("r-ggplot2" ,r-ggplot2)
4661 ("r-iranges" ,r-iranges)
4662 ("r-purrr" ,r-purrr)
4663 ("r-rtracklayer" ,r-rtracklayer)
4664 ("r-s4vectors" ,r-s4vectors)))
4665 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4666 (synopsis "Make read coverage plots from BigWig files")
4668 "This package provides tools to visualize read coverage from sequencing
4669 experiments together with genomic annotations (genes, transcripts, peaks).
4670 Introns of long transcripts can be rescaled to a fixed length for better
4671 visualization of exonic read coverage.")
4672 (license license:asl2.0)))
4674 (define-public r-widgettools
4676 (name "r-widgettools")
4681 (uri (bioconductor-uri "widgetTools" version))
4684 "1nqy3icayacv5mlv5s5xgfli0dqzancs6zpffrl5p237c994nyr5"))))
4685 (properties `((upstream-name . "widgetTools")))
4686 (build-system r-build-system)
4687 (home-page "https://bioconductor.org/packages/widgetTools/")
4688 (synopsis "Tools for creating interactive tcltk widgets")
4690 "This package contains tools to support the construction of tcltk
4692 ;; Any version of the LGPL.
4693 (license license:lgpl3+)))
4695 (define-public r-webbioc
4702 (uri (bioconductor-uri "webbioc" version))
4705 "1cwrmvh1l603k6j1r425c4vrqp0zf0x7bgx7y1wnbq4r7yc5sp62"))))
4706 (build-system r-build-system)
4708 `(("netpbm" ,netpbm)
4711 `(("r-affy" ,r-affy)
4712 ("r-annaffy" ,r-annaffy)
4713 ("r-biobase" ,r-biobase)
4714 ("r-biocmanager" ,r-biocmanager)
4715 ("r-gcrma" ,r-gcrma)
4716 ("r-multtest" ,r-multtest)
4717 ("r-qvalue" ,r-qvalue)
4719 (home-page "https://www.bioconductor.org/")
4720 (synopsis "Bioconductor web interface")
4722 "This package provides an integrated web interface for doing microarray
4723 analysis using several of the Bioconductor packages. It is intended to be
4724 deployed as a centralized bioinformatics resource for use by many users.
4725 Currently only Affymetrix oligonucleotide analysis is supported.")
4726 (license license:gpl2+)))
4728 (define-public r-zfpkm
4735 (uri (bioconductor-uri "zFPKM" version))
4738 "1hg0vc0ns8d4jpddn1v5a5m13a033b0wf1al01pb1lvmx5mzzr2n"))))
4739 (properties `((upstream-name . "zFPKM")))
4740 (build-system r-build-system)
4742 `(("r-checkmate" ,r-checkmate)
4743 ("r-dplyr" ,r-dplyr)
4744 ("r-ggplot2" ,r-ggplot2)
4745 ("r-summarizedexperiment" ,r-summarizedexperiment)
4746 ("r-tidyr" ,r-tidyr)))
4747 (home-page "https://github.com/ronammar/zFPKM/")
4748 (synopsis "Functions to facilitate zFPKM transformations")
4750 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
4751 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
4753 (license license:gpl3)))
4755 (define-public r-rbowtie2
4762 (uri (bioconductor-uri "Rbowtie2" version))
4765 "1b7x42n9zisi2w2wwfc0c39j8s9868imyr0ysqgswf6l5mv9ivc5"))))
4766 (properties `((upstream-name . "Rbowtie2")))
4767 (build-system r-build-system)
4770 (home-page "https://bioconductor.org/packages/Rbowtie2/")
4771 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
4773 "This package provides an R wrapper of the popular @code{bowtie2}
4774 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
4775 rapid adapter trimming, identification, and read merging.")
4776 (license license:gpl3+)))
4778 (define-public r-progeny
4785 (uri (bioconductor-uri "progeny" version))
4788 "0j3kxjj7xmmwb29p87n3bw7bl38gcb94jrpw32126a578rf1pfrq"))))
4789 (build-system r-build-system)
4790 (propagated-inputs `(("r-biobase" ,r-biobase)))
4791 (home-page "https://github.com/saezlab/progeny")
4792 (synopsis "Pathway responsive gene activity inference")
4794 "This package provides a function to infer pathway activity from gene
4795 expression. It contains the linear model inferred in the publication
4796 \"Perturbation-response genes reveal signaling footprints in cancer gene
4798 (license license:asl2.0)))
4800 (define-public r-arrmnormalization
4802 (name "r-arrmnormalization")
4807 (uri (bioconductor-uri "ARRmNormalization" version))
4810 "0jj81q454nyh4hr5c56q1hv7i4ynx3rwnvpv08w34a6m77122bi1"))))
4812 `((upstream-name . "ARRmNormalization")))
4813 (build-system r-build-system)
4814 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
4815 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
4816 (synopsis "Adaptive robust regression normalization for methylation data")
4818 "This is a package to perform the @dfn{Adaptive Robust Regression
4819 method} (ARRm) for the normalization of methylation data from the Illumina
4820 Infinium HumanMethylation 450k assay.")
4821 (license license:artistic2.0)))
4823 (define-public r-biocfilecache
4825 (name "r-biocfilecache")
4830 (uri (bioconductor-uri "BiocFileCache" version))
4833 "0jivhn95y6zv5ryamqk6nyd4l8nlskq64j362l9ml9qw746v0ja6"))))
4834 (properties `((upstream-name . "BiocFileCache")))
4835 (build-system r-build-system)
4837 `(("r-curl" ,r-curl)
4839 ("r-dbplyr" ,r-dbplyr)
4840 ("r-dplyr" ,r-dplyr)
4842 ("r-rappdirs" ,r-rappdirs)
4843 ("r-rsqlite" ,r-rsqlite)))
4844 (home-page "https://bioconductor.org/packages/BiocFileCache/")
4845 (synopsis "Manage files across sessions")
4847 "This package creates a persistent on-disk cache of files that the user
4848 can add, update, and retrieve. It is useful for managing resources (such as
4849 custom Txdb objects) that are costly or difficult to create, web resources,
4850 and data files used across sessions.")
4851 (license license:artistic2.0)))
4853 (define-public r-iclusterplus
4855 (name "r-iclusterplus")
4860 (uri (bioconductor-uri "iClusterPlus" version))
4863 "1dzgfzf2x8m62hssvsn1zzag7m444kyxj2vpdxl9nk859dr5pf37"))))
4864 (properties `((upstream-name . "iClusterPlus")))
4865 (build-system r-build-system)
4866 (native-inputs `(("gfortran" ,gfortran)))
4867 (home-page "https://bioconductor.org/packages/iClusterPlus/")
4868 (synopsis "Integrative clustering of multi-type genomic data")
4870 "iClusterPlus is developed for integrative clustering analysis of
4871 multi-type genomic data and is an enhanced version of iCluster proposed and
4872 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
4873 from the experiments where biological samples (e.g. tumor samples) are
4874 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
4875 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
4876 on. In the iClusterPlus model, binary observations such as somatic mutation
4877 are modeled as Binomial processes; categorical observations such as copy
4878 number states are realizations of Multinomial random variables; counts are
4879 modeled as Poisson random processes; and continuous measures are modeled by
4880 Gaussian distributions.")
4881 (license license:gpl2+)))
4883 (define-public r-rbowtie
4890 (uri (bioconductor-uri "Rbowtie" version))
4893 "0yy31xhdmf6xb21wlhmxxwfqpm0nil39pb2cs3pq5ia758lb88z4"))))
4894 (properties `((upstream-name . "Rbowtie")))
4895 (build-system r-build-system)
4898 (home-page "https://bioconductor.org/packages/Rbowtie/")
4899 (synopsis "R bowtie wrapper")
4901 "This package provides an R wrapper around the popular bowtie short read
4902 aligner and around SpliceMap, a de novo splice junction discovery and
4904 (license license:artistic2.0)))
4906 (define-public r-sgseq
4913 (uri (bioconductor-uri "SGSeq" version))
4916 "0950iv08wd0kjaw55rjn7m6syklvrabwr2zqq74wzyc5afyk2mrw"))))
4917 (properties `((upstream-name . "SGSeq")))
4918 (build-system r-build-system)
4920 `(("r-annotationdbi" ,r-annotationdbi)
4921 ("r-biocgenerics" ,r-biocgenerics)
4922 ("r-biostrings" ,r-biostrings)
4923 ("r-genomeinfodb" ,r-genomeinfodb)
4924 ("r-genomicalignments" ,r-genomicalignments)
4925 ("r-genomicfeatures" ,r-genomicfeatures)
4926 ("r-genomicranges" ,r-genomicranges)
4927 ("r-igraph" ,r-igraph)
4928 ("r-iranges" ,r-iranges)
4929 ("r-rsamtools" ,r-rsamtools)
4930 ("r-rtracklayer" ,r-rtracklayer)
4931 ("r-runit" ,r-runit)
4932 ("r-s4vectors" ,r-s4vectors)
4933 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4934 (home-page "https://bioconductor.org/packages/SGSeq/")
4935 (synopsis "Splice event prediction and quantification from RNA-seq data")
4937 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
4938 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
4939 represented as a splice graph, which can be obtained from existing annotation
4940 or predicted from the mapped sequence reads. Splice events are identified
4941 from the graph and are quantified locally using structurally compatible reads
4942 at the start or end of each splice variant. The software includes functions
4943 for splice event prediction, quantification, visualization and
4945 (license license:artistic2.0)))
4947 (define-public r-rhisat2
4954 (uri (bioconductor-uri "Rhisat2" version))
4957 "02fn5cm8sj2s9x00505y3iyipn1r3lpvpwpjy2pdxdbpmhb5hy49"))))
4958 (properties `((upstream-name . "Rhisat2")))
4959 (build-system r-build-system)
4962 (modify-phases %standard-phases
4963 (add-after 'unpack 'make-reproducible
4965 (substitute* "src/Makefile"
4966 (("`hostname`") "guix")
4968 ;; Avoid shelling out to "which".
4969 (("^CC =.*") (which "gcc"))
4970 (("^CPP =.*") (which "g++")))
4973 `(("r-genomicfeatures" ,r-genomicfeatures)
4974 ("r-genomicranges" ,r-genomicranges)
4975 ("r-sgseq" ,r-sgseq)))
4976 (home-page "https://github.com/fmicompbio/Rhisat2")
4977 (synopsis "R Wrapper for HISAT2 sequence aligner")
4979 "This package provides an R interface to the HISAT2 spliced short-read
4980 aligner by Kim et al. (2015). The package contains wrapper functions to
4981 create a genome index and to perform the read alignment to the generated
4983 (license license:gpl3)))
4985 (define-public r-quasr
4992 (uri (bioconductor-uri "QuasR" version))
4995 "07m5q7wasapj2984kwy897510flbhvz7x0fgs7q2vm5wjhfzdrgv"))))
4996 (properties `((upstream-name . "QuasR")))
4997 (build-system r-build-system)
5001 `(("r-annotationdbi" ,r-annotationdbi)
5002 ("r-biobase" ,r-biobase)
5003 ("r-biocgenerics" ,r-biocgenerics)
5004 ("r-biocmanager" ,r-biocmanager)
5005 ("r-biocparallel" ,r-biocparallel)
5006 ("r-biostrings" ,r-biostrings)
5007 ("r-bsgenome" ,r-bsgenome)
5008 ("r-genomeinfodb" ,r-genomeinfodb)
5009 ("r-genomicalignments" ,r-genomicalignments)
5010 ("r-genomicfeatures" ,r-genomicfeatures)
5011 ("r-genomicfiles" ,r-genomicfiles)
5012 ("r-genomicranges" ,r-genomicranges)
5013 ("r-iranges" ,r-iranges)
5014 ("r-rbowtie" ,r-rbowtie)
5015 ("r-rhisat2" ,r-rhisat2)
5016 ("r-rhtslib" ,r-rhtslib)
5017 ("r-rsamtools" ,r-rsamtools)
5018 ("r-rtracklayer" ,r-rtracklayer)
5019 ("r-s4vectors" ,r-s4vectors)
5020 ("r-shortread" ,r-shortread)))
5021 (home-page "https://bioconductor.org/packages/QuasR/")
5022 (synopsis "Quantify and annotate short reads in R")
5024 "This package provides a framework for the quantification and analysis of
5025 short genomic reads. It covers a complete workflow starting from raw sequence
5026 reads, over creation of alignments and quality control plots, to the
5027 quantification of genomic regions of interest.")
5028 (license license:gpl2)))
5030 (define-public r-rqc
5037 (uri (bioconductor-uri "Rqc" version))
5040 "1nxkrb9kx41g050yz935yrl9pjkakhr8v6whxcvr72gg4r9m2x3m"))))
5041 (properties `((upstream-name . "Rqc")))
5042 (build-system r-build-system)
5044 `(("r-biocgenerics" ,r-biocgenerics)
5045 ("r-biocparallel" ,r-biocparallel)
5046 ("r-biocstyle" ,r-biocstyle)
5047 ("r-biostrings" ,r-biostrings)
5048 ("r-biovizbase" ,r-biovizbase)
5049 ("r-genomicalignments" ,r-genomicalignments)
5050 ("r-genomicfiles" ,r-genomicfiles)
5051 ("r-ggplot2" ,r-ggplot2)
5052 ("r-iranges" ,r-iranges)
5053 ("r-knitr" ,r-knitr)
5054 ("r-markdown" ,r-markdown)
5057 ("r-reshape2" ,r-reshape2)
5058 ("r-rsamtools" ,r-rsamtools)
5059 ("r-s4vectors" ,r-s4vectors)
5060 ("r-shiny" ,r-shiny)
5061 ("r-shortread" ,r-shortread)))
5062 (home-page "https://github.com/labbcb/Rqc")
5063 (synopsis "Quality control tool for high-throughput sequencing data")
5065 "Rqc is an optimized tool designed for quality control and assessment of
5066 high-throughput sequencing data. It performs parallel processing of entire
5067 files and produces a report which contains a set of high-resolution
5069 (license license:gpl2+)))
5071 (define-public r-birewire
5078 (uri (bioconductor-uri "BiRewire" version))
5081 "1074cp422ail72yajn8p0bg26h6zzz07nzypnwfyv86qrpvpdw9q"))))
5082 (properties `((upstream-name . "BiRewire")))
5083 (build-system r-build-system)
5085 `(("r-igraph" ,r-igraph)
5086 ("r-matrix" ,r-matrix)
5088 ("r-tsne" ,r-tsne)))
5089 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5090 (synopsis "Tools for randomization of bipartite graphs")
5092 "This package provides functions for bipartite network rewiring through N
5093 consecutive switching steps and for the computation of the minimal number of
5094 switching steps to be performed in order to maximise the dissimilarity with
5095 respect to the original network. It includes functions for the analysis of
5096 the introduced randomness across the switching steps and several other
5097 routines to analyse the resulting networks and their natural projections.")
5098 (license license:gpl3)))
5100 (define-public r-birta
5107 (uri (bioconductor-uri "birta" version))
5110 "1zhlwapdgkz0fpv5bqfxh9aw6ymnmxnnm1r0n0kfzn5izyjavslg"))))
5111 (build-system r-build-system)
5113 `(("r-biobase" ,r-biobase)
5114 ("r-limma" ,r-limma)
5115 ("r-mass" ,r-mass)))
5116 (home-page "https://bioconductor.org/packages/birta")
5117 (synopsis "Bayesian inference of regulation of transcriptional activity")
5119 "Expression levels of mRNA molecules are regulated by different
5120 processes, comprising inhibition or activation by transcription factors and
5121 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5122 Inference of Regulation of Transcriptional Activity) uses the regulatory
5123 networks of transcription factors and miRNAs together with mRNA and miRNA
5124 expression data to predict switches in regulatory activity between two
5125 conditions. A Bayesian network is used to model the regulatory structure and
5126 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5127 (license license:gpl2+)))
5129 (define-public r-multidataset
5131 (name "r-multidataset")
5136 (uri (bioconductor-uri "MultiDataSet" version))
5139 "0iw99ymrv3ls023mpmgyagmb5simgsgadpj0k4bnssfaqnklywlj"))))
5140 (properties `((upstream-name . "MultiDataSet")))
5141 (build-system r-build-system)
5143 `(("r-biobase" ,r-biobase)
5144 ("r-biocgenerics" ,r-biocgenerics)
5145 ("r-genomicranges" ,r-genomicranges)
5146 ("r-ggplot2" ,r-ggplot2)
5147 ("r-ggrepel" ,r-ggrepel)
5148 ("r-iranges" ,r-iranges)
5149 ("r-limma" ,r-limma)
5150 ("r-qqman" ,r-qqman)
5151 ("r-s4vectors" ,r-s4vectors)
5152 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5153 (home-page "https://bioconductor.org/packages/MultiDataSet/")
5154 (synopsis "Implementation of MultiDataSet and ResultSet")
5156 "This package provides an implementation of the BRGE's (Bioinformatic
5157 Research Group in Epidemiology from Center for Research in Environmental
5158 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
5159 integrating multi omics data sets and ResultSet is a container for omics
5160 results. This package contains base classes for MEAL and rexposome
5162 (license license:expat)))
5164 (define-public r-ropls
5171 (uri (bioconductor-uri "ropls" version))
5174 "1sm2fmygrra9gdcs90lmk5y1ag6arga6159kggx4ij8bkhyc66vb"))))
5175 (build-system r-build-system)
5177 `(("r-biobase" ,r-biobase)
5178 ("r-multidataset" ,r-multidataset)))
5180 `(("r-knitr" ,r-knitr))) ; for vignettes
5181 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5182 (synopsis "Multivariate analysis and feature selection of omics data")
5184 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5185 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5186 regression, classification, and feature selection of omics data where the
5187 number of variables exceeds the number of samples and with multicollinearity
5188 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5189 separately model the variation correlated (predictive) to the factor of
5190 interest and the uncorrelated (orthogonal) variation. While performing
5191 similarly to PLS, OPLS facilitates interpretation.
5193 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5194 analysis and feature selection of omics data. In addition to scores, loadings
5195 and weights plots, the package provides metrics and graphics to determine the
5196 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5197 validity of the model by permutation testing, detect outliers, and perform
5198 feature selection (e.g. with Variable Importance in Projection or regression
5200 (license license:cecill)))
5202 (define-public r-biosigner
5204 (name "r-biosigner")
5209 (uri (bioconductor-uri "biosigner" version))
5212 "1kdfhw629qczrfms0jmphqz0ksjzi8js00xj92h1lnv092npfk0j"))))
5213 (build-system r-build-system)
5215 `(("r-biobase" ,r-biobase)
5216 ("r-e1071" ,r-e1071)
5217 ("r-multidataset" ,r-multidataset)
5218 ("r-randomforest" ,r-randomforest)
5219 ("r-ropls" ,r-ropls)))
5221 `(("r-knitr" ,r-knitr)
5222 ("r-rmarkdown" ,r-rmarkdown)
5223 ("pandoc" ,ghc-pandoc)
5224 ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
5225 (home-page "https://bioconductor.org/packages/biosigner/")
5226 (synopsis "Signature discovery from omics data")
5228 "Feature selection is critical in omics data analysis to extract
5229 restricted and meaningful molecular signatures from complex and high-dimension
5230 data, and to build robust classifiers. This package implements a method to
5231 assess the relevance of the variables for the prediction performances of the
5232 classifier. The approach can be run in parallel with the PLS-DA, Random
5233 Forest, and SVM binary classifiers. The signatures and the corresponding
5234 'restricted' models are returned, enabling future predictions on new
5236 (license license:cecill)))
5238 (define-public r-annotatr
5245 (uri (bioconductor-uri "annotatr" version))
5248 "1bibk3p1q4cavqy11xs6rqqhqdjsq2dd7lf7blwcr27s5ajcd6dj"))))
5249 (build-system r-build-system)
5251 `(("r-annotationdbi" ,r-annotationdbi)
5252 ("r-annotationhub" ,r-annotationhub)
5253 ("r-dplyr" ,r-dplyr)
5254 ("r-genomeinfodb" ,r-genomeinfodb)
5255 ("r-genomicfeatures" ,r-genomicfeatures)
5256 ("r-genomicranges" ,r-genomicranges)
5257 ("r-ggplot2" ,r-ggplot2)
5258 ("r-iranges" ,r-iranges)
5259 ("r-readr" ,r-readr)
5260 ("r-regioner" ,r-regioner)
5261 ("r-reshape2" ,r-reshape2)
5262 ("r-rtracklayer" ,r-rtracklayer)
5263 ("r-s4vectors" ,r-s4vectors)))
5264 (home-page "https://bioconductor.org/packages/annotatr/")
5265 (synopsis "Annotation of genomic regions to genomic annotations")
5267 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5268 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5269 to investigate the intersecting genomic annotations. Such annotations include
5270 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5271 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5272 enhancers. The annotatr package provides an easy way to summarize and
5273 visualize the intersection of genomic sites/regions with genomic
5275 (license license:gpl3)))
5277 (define-public r-rsubread
5284 (uri (bioconductor-uri "Rsubread" version))
5287 "0l8q9y2a4m1di0w5nlxhq9jgliinhgr2fwjpm5ixnqx5j3iprlwd"))))
5288 (properties `((upstream-name . "Rsubread")))
5289 (build-system r-build-system)
5290 (inputs `(("zlib" ,zlib)))
5291 (home-page "https://bioconductor.org/packages/Rsubread/")
5292 (synopsis "Subread sequence alignment and counting for R")
5294 "This package provides tools for alignment, quantification and analysis
5295 of second and third generation sequencing data. It includes functionality for
5296 read mapping, read counting, SNP calling, structural variant detection and
5297 gene fusion discovery. It can be applied to all major sequencing techologies
5298 and to both short and long sequence reads.")
5299 (license license:gpl3)))
5301 (define-public r-flowutils
5303 (name "r-flowutils")
5308 (uri (bioconductor-uri "flowUtils" version))
5311 "1xcs19j9p3izvksyy5wzsbicwby0dsa9g2w7gjzwynzgj5dpfr81"))))
5312 (properties `((upstream-name . "flowUtils")))
5313 (build-system r-build-system)
5315 `(("r-biobase" ,r-biobase)
5316 ("r-corpcor" ,r-corpcor)
5317 ("r-flowcore" ,r-flowcore)
5318 ("r-graph" ,r-graph)
5319 ("r-runit" ,r-runit)
5321 (home-page "https://github.com/jspidlen/flowUtils")
5322 (synopsis "Utilities for flow cytometry")
5324 "This package provides utilities for flow cytometry data.")
5325 (license license:artistic2.0)))
5327 (define-public r-consensusclusterplus
5329 (name "r-consensusclusterplus")
5334 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5337 "0pnh5zy6d3c364xxjdn5zp3kf5afhsxv6yzkdn1qspny0pmqlrp4"))))
5339 `((upstream-name . "ConsensusClusterPlus")))
5340 (build-system r-build-system)
5343 ("r-biobase" ,r-biobase)
5344 ("r-cluster" ,r-cluster)))
5345 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5346 (synopsis "Clustering algorithm")
5348 "This package provides an implementation of an algorithm for determining
5349 cluster count and membership by stability evidence in unsupervised analysis.")
5350 (license license:gpl2)))
5352 (define-public r-cytolib
5359 (uri (bioconductor-uri "cytolib" version))
5362 "1zk5i09k782lw6297gl3rh0g4fxswr2ang8dgqj7p0814l7h15k9"))))
5363 (properties `((upstream-name . "cytolib")))
5364 (build-system r-build-system)
5365 (home-page "https://bioconductor.org/packages/cytolib/")
5366 (synopsis "C++ infrastructure for working with gated cytometry")
5368 "This package provides the core data structure and API to represent and
5369 interact with gated cytometry data.")
5370 (license license:artistic2.0)))
5372 (define-public r-flowcore
5379 (uri (bioconductor-uri "flowCore" version))
5382 "08kvxc187iwlixibx1860jcp5g9bsw8abkv06x2qv1w83fas4pp2"))))
5383 (properties `((upstream-name . "flowCore")))
5384 (build-system r-build-system)
5387 ("r-biobase" ,r-biobase)
5388 ("r-biocgenerics" ,r-biocgenerics)
5389 ("r-cytolib" ,r-cytolib)
5390 ("r-matrixstats" ,r-matrixstats)
5391 ("r-rcpp" ,r-rcpp)))
5392 (home-page "https://bioconductor.org/packages/flowCore")
5393 (synopsis "Basic structures for flow cytometry data")
5395 "This package provides S4 data structures and basic functions to deal
5396 with flow cytometry data.")
5397 (license license:artistic2.0)))
5399 (define-public r-flowmeans
5401 (name "r-flowmeans")
5406 (uri (bioconductor-uri "flowMeans" version))
5409 "1yisrikaafmpb4sig2c5l0wcz4idrs4as7i9x90v6z2v94iq0m8h"))))
5410 (properties `((upstream-name . "flowMeans")))
5411 (build-system r-build-system)
5413 `(("r-biobase" ,r-biobase)
5414 ("r-feature" ,r-feature)
5415 ("r-flowcore" ,r-flowcore)
5416 ("r-rrcov" ,r-rrcov)))
5417 (home-page "https://bioconductor.org/packages/flowMeans")
5418 (synopsis "Non-parametric flow cytometry data gating")
5420 "This package provides tools to identify cell populations in Flow
5421 Cytometry data using non-parametric clustering and segmented-regression-based
5422 change point detection.")
5423 (license license:artistic2.0)))
5425 (define-public r-ncdfflow
5432 (uri (bioconductor-uri "ncdfFlow" version))
5435 "06lscx6h4rg80ifi90rj7z2497b8w1fjipm3l8s3230rkizhh02i"))))
5436 (properties `((upstream-name . "ncdfFlow")))
5437 (build-system r-build-system)
5442 ("r-biobase" ,r-biobase)
5443 ("r-biocgenerics" ,r-biocgenerics)
5444 ("r-flowcore" ,r-flowcore)
5446 ("r-rcpparmadillo" ,r-rcpparmadillo)
5447 ("r-rhdf5lib" ,r-rhdf5lib)
5448 ("r-zlibbioc" ,r-zlibbioc)))
5449 (home-page "https://bioconductor.org/packages/ncdfFlow/")
5450 (synopsis "HDF5 based storage for flow cytometry data")
5452 "This package provides HDF5 storage based methods and functions for
5453 manipulation of flow cytometry data.")
5454 (license license:artistic2.0)))
5456 (define-public r-ggcyto
5463 (uri (bioconductor-uri "ggcyto" version))
5466 "165qszvy5z176h1l3dnjb5dcm279b6bjl5n5gzz8wfn4xpn8anc8"))))
5467 (properties `((upstream-name . "ggcyto")))
5468 (build-system r-build-system)
5470 `(("r-data-table" ,r-data-table)
5471 ("r-flowcore" ,r-flowcore)
5472 ("r-flowworkspace" ,r-flowworkspace)
5473 ("r-ggplot2" ,r-ggplot2)
5474 ("r-gridextra" ,r-gridextra)
5475 ("r-ncdfflow" ,r-ncdfflow)
5477 ("r-rcolorbrewer" ,r-rcolorbrewer)
5478 ("r-rlang" ,r-rlang)
5479 ("r-scales" ,r-scales)))
5480 (home-page "https://github.com/RGLab/ggcyto/issues")
5481 (synopsis "Visualize Cytometry data with ggplot")
5483 "With the dedicated fortify method implemented for @code{flowSet},
5484 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
5485 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
5486 and some custom layers also make it easy to add gates and population
5487 statistics to the plot.")
5488 (license license:artistic2.0)))
5490 (define-public r-flowviz
5497 (uri (bioconductor-uri "flowViz" version))
5500 "0ik16bxcfcg3q26ra3055718kskid64aaazcbqsxalca9ppdm4k7"))))
5501 (properties `((upstream-name . "flowViz")))
5502 (build-system r-build-system)
5504 `(("r-biobase" ,r-biobase)
5505 ("r-flowcore" ,r-flowcore)
5506 ("r-hexbin" ,r-hexbin)
5507 ("r-idpmisc" ,r-idpmisc)
5508 ("r-kernsmooth" ,r-kernsmooth)
5509 ("r-lattice" ,r-lattice)
5510 ("r-latticeextra" ,r-latticeextra)
5512 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5513 (home-page "https://bioconductor.org/packages/flowViz/")
5514 (synopsis "Visualization for flow cytometry")
5516 "This package provides visualization tools for flow cytometry data.")
5517 (license license:artistic2.0)))
5519 (define-public r-flowclust
5521 (name "r-flowclust")
5526 (uri (bioconductor-uri "flowClust" version))
5529 "0k4bgc4mf512njfdfg5ld9l7slgfxyfh766jab87j96zrrgcnj8s"))))
5530 (properties `((upstream-name . "flowClust")))
5531 (build-system r-build-system)
5534 (list "--configure-args=--enable-bundled-gsl=no")))
5536 `(("r-biobase" ,r-biobase)
5537 ("r-biocgenerics" ,r-biocgenerics)
5539 ("r-corpcor" ,r-corpcor)
5540 ("r-ellipse" ,r-ellipse)
5541 ("r-flowcore" ,r-flowcore)
5542 ("r-flowviz" ,r-flowviz)
5543 ("r-graph" ,r-graph)
5544 ("r-mnormt" ,r-mnormt)))
5548 `(("pkg-config" ,pkg-config)))
5549 (home-page "https://bioconductor.org/packages/flowClust")
5550 (synopsis "Clustering for flow cytometry")
5552 "This package provides robust model-based clustering using a t-mixture
5553 model with Box-Cox transformation.")
5554 (license license:artistic2.0)))
5556 ;; TODO: this package bundles an old version of protobuf. It's not easy to
5557 ;; make it use our protobuf package instead.
5558 (define-public r-rprotobuflib
5560 (name "r-rprotobuflib")
5565 (uri (bioconductor-uri "RProtoBufLib" version))
5568 "0dlgki21a37bxqh3cf83vl5zqxm86472g8a9plvhrjzzsn3mwnrm"))))
5569 (properties `((upstream-name . "RProtoBufLib")))
5570 (build-system r-build-system)
5573 (modify-phases %standard-phases
5574 (add-after 'unpack 'unpack-bundled-sources
5576 (with-directory-excursion "src"
5577 (invoke "tar" "xf" "protobuf-2.6.0.tgz"))
5579 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
5580 (synopsis "C++ headers and static libraries of Protocol buffers")
5582 "This package provides the headers and static library of Protocol buffers
5583 for other R packages to compile and link against.")
5584 (license license:bsd-3)))
5586 (define-public r-flowworkspace
5588 (name "r-flowworkspace")
5593 (uri (bioconductor-uri "flowWorkspace" version))
5596 "1ijbc6z9ljhrw3cqr02smgplhrfg44gzrb1dq4gbrpq3nj4khhpn"))))
5597 (properties `((upstream-name . "flowWorkspace")))
5598 (build-system r-build-system)
5601 ("r-biobase" ,r-biobase)
5602 ("r-biocgenerics" ,r-biocgenerics)
5603 ("r-cytolib" ,r-cytolib)
5604 ("r-data-table" ,r-data-table)
5605 ("r-digest" ,r-digest)
5606 ("r-dplyr" ,r-dplyr)
5607 ("r-flowcore" ,r-flowcore)
5608 ("r-flowviz" ,r-flowviz)
5609 ("r-graph" ,r-graph)
5610 ("r-gridextra" ,r-gridextra)
5611 ("r-lattice" ,r-lattice)
5612 ("r-latticeextra" ,r-latticeextra)
5613 ("r-matrixstats" ,r-matrixstats)
5614 ("r-ncdfflow" ,r-ncdfflow)
5616 ("r-rcolorbrewer" ,r-rcolorbrewer)
5618 ("r-rcppparallel" ,r-rcppparallel)
5619 ("r-rgraphviz" ,r-rgraphviz)
5620 ("r-rprotobuflib" ,r-rprotobuflib)
5621 ("r-scales" ,r-scales)
5622 ("r-stringr" ,r-stringr)))
5623 (home-page "https://bioconductor.org/packages/flowWorkspace/")
5624 (synopsis "Infrastructure for working with cytometry data")
5626 "This package is designed to facilitate comparison of automated gating
5627 methods against manual gating done in flowJo. This package allows you to
5628 import basic flowJo workspaces into BioConductor and replicate the gating from
5629 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
5630 samples, compensation, and transformation are performed so that the output
5631 matches the flowJo analysis.")
5632 (license license:artistic2.0)))
5634 (define-public r-flowstats
5636 (name "r-flowstats")
5641 (uri (bioconductor-uri "flowStats" version))
5644 "0pql0lpf90nra7w6z6nd8l9cgjlsg2pxysfravnbzfhl3pjvd96w"))))
5645 (properties `((upstream-name . "flowStats")))
5646 (build-system r-build-system)
5648 `(("r-biobase" ,r-biobase)
5649 ("r-biocgenerics" ,r-biocgenerics)
5650 ("r-cluster" ,r-cluster)
5652 ("r-flowcore" ,r-flowcore)
5653 ("r-flowviz" ,r-flowviz)
5654 ("r-flowworkspace" ,r-flowworkspace)
5655 ("r-kernsmooth" ,r-kernsmooth)
5657 ("r-lattice" ,r-lattice)
5659 ("r-ncdfflow" ,r-ncdfflow)
5660 ("r-rcolorbrewer" ,r-rcolorbrewer)
5661 ("r-rrcov" ,r-rrcov)))
5662 (home-page "http://www.github.com/RGLab/flowStats")
5663 (synopsis "Statistical methods for the analysis of flow cytometry data")
5665 "This package provides methods and functionality to analyze flow data
5666 that is beyond the basic infrastructure provided by the @code{flowCore}
5668 (license license:artistic2.0)))
5670 (define-public r-opencyto
5677 (uri (bioconductor-uri "openCyto" version))
5680 "0h25nhvq1zq624wsgb55wjcgri9rcd2fnqkb31h9jdakr01dw2sb"))))
5681 (properties `((upstream-name . "openCyto")))
5682 (build-system r-build-system)
5684 `(("r-biobase" ,r-biobase)
5685 ("r-biocgenerics" ,r-biocgenerics)
5687 ("r-data-table" ,r-data-table)
5688 ("r-flowclust" ,r-flowclust)
5689 ("r-flowcore" ,r-flowcore)
5690 ("r-flowstats" ,r-flowstats)
5691 ("r-flowviz" ,r-flowviz)
5692 ("r-flowworkspace" ,r-flowworkspace)
5693 ("r-graph" ,r-graph)
5694 ("r-gtools" ,r-gtools)
5696 ("r-lattice" ,r-lattice)
5698 ("r-ncdfflow" ,r-ncdfflow)
5700 ("r-r-utils" ,r-r-utils)
5702 ("r-rcolorbrewer" ,r-rcolorbrewer)
5704 ("r-rrcov" ,r-rrcov)))
5705 (home-page "https://bioconductor.org/packages/openCyto")
5706 (synopsis "Hierarchical gating pipeline for flow cytometry data")
5708 "This package is designed to facilitate the automated gating methods in a
5709 sequential way to mimic the manual gating strategy.")
5710 (license license:artistic2.0)))
5712 (define-public r-cytoml
5719 (uri (bioconductor-uri "CytoML" version))
5722 "0m8x18wkvis85cawv7j07pk59w76wnzy93ia99gd24j82z4h97p1"))))
5723 (properties `((upstream-name . "CytoML")))
5724 (build-system r-build-system)
5726 `(("libxml2" ,libxml2)))
5728 `(("r-base64enc" ,r-base64enc)
5730 ("r-biobase" ,r-biobase)
5731 ("r-corpcor" ,r-corpcor)
5732 ("r-cytolib" ,r-cytolib)
5733 ("r-data-table" ,r-data-table)
5734 ("r-dplyr" ,r-dplyr)
5735 ("r-flowcore" ,r-flowcore)
5736 ("r-flowworkspace" ,r-flowworkspace)
5737 ("r-ggcyto" ,r-ggcyto)
5738 ("r-graph" ,r-graph)
5739 ("r-jsonlite" ,r-jsonlite)
5740 ("r-lattice" ,r-lattice)
5741 ("r-ncdfflow" ,r-ncdfflow)
5742 ("r-opencyto" ,r-opencyto)
5746 ("r-rcppparallel" ,r-rcppparallel)
5747 ("r-rgraphviz" ,r-rgraphviz)
5748 ("r-rprotobuflib" ,r-rprotobuflib)
5749 ("r-runit" ,r-runit)
5751 ("r-yaml" ,r-yaml)))
5752 (home-page "https://github.com/RGLab/CytoML")
5753 (synopsis "GatingML interface for cross platform cytometry data sharing")
5755 "This package provides an interface to implementations of the GatingML2.0
5756 standard to exchange gated cytometry data with other software platforms.")
5757 (license license:artistic2.0)))
5759 (define-public r-flowsom
5766 (uri (bioconductor-uri "FlowSOM" version))
5769 "0265sq4zvj6d6h5ghqj9xzm4b0z9v65kgyl88cgdcpdkzfnfcvd5"))))
5770 (properties `((upstream-name . "FlowSOM")))
5771 (build-system r-build-system)
5773 `(("r-biocgenerics" ,r-biocgenerics)
5774 ("r-consensusclusterplus" ,r-consensusclusterplus)
5775 ("r-cytoml" ,r-cytoml)
5776 ("r-flowcore" ,r-flowcore)
5777 ("r-flowworkspace" ,r-flowworkspace)
5778 ("r-igraph" ,r-igraph)
5779 ("r-rcolorbrewer" ,r-rcolorbrewer)
5782 (home-page "https://bioconductor.org/packages/FlowSOM/")
5783 (synopsis "Visualize and interpret cytometry data")
5785 "FlowSOM offers visualization options for cytometry data, by using
5786 self-organizing map clustering and minimal spanning trees.")
5787 (license license:gpl2+)))
5789 (define-public r-mixomics
5796 (uri (bioconductor-uri "mixOmics" version))
5799 "18jwrdyc4pnx917y1kskxz3fqvlrkyy4ny0xqrfcidz0j7p0b7wr"))))
5800 (properties `((upstream-name . "mixOmics")))
5801 (build-system r-build-system)
5803 `(("r-corpcor" ,r-corpcor)
5804 ("r-dplyr" ,r-dplyr)
5805 ("r-ellipse" ,r-ellipse)
5806 ("r-ggplot2" ,r-ggplot2)
5807 ("r-gridextra" ,r-gridextra)
5808 ("r-igraph" ,r-igraph)
5809 ("r-lattice" ,r-lattice)
5811 ("r-matrixstats" ,r-matrixstats)
5812 ("r-rarpack" ,r-rarpack)
5813 ("r-rcolorbrewer" ,r-rcolorbrewer)
5814 ("r-reshape2" ,r-reshape2)
5815 ("r-tidyr" ,r-tidyr)))
5816 (home-page "http://www.mixOmics.org")
5817 (synopsis "Multivariate methods for exploration of biological datasets")
5819 "mixOmics offers a wide range of multivariate methods for the exploration
5820 and integration of biological datasets with a particular focus on variable
5821 selection. The package proposes several sparse multivariate models we have
5822 developed to identify the key variables that are highly correlated, and/or
5823 explain the biological outcome of interest. The data that can be analysed
5824 with mixOmics may come from high throughput sequencing technologies, such as
5825 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
5826 also beyond the realm of omics (e.g. spectral imaging). The methods
5827 implemented in mixOmics can also handle missing values without having to
5828 delete entire rows with missing data.")
5829 (license license:gpl2+)))
5831 (define-public r-depecher
5838 (uri (bioconductor-uri "DepecheR" version))
5841 "1f6zbc0fq7xjflh3mkjx1n83mpppw663dj22rlpxzwp1kpmf6wm5"))))
5842 (properties `((upstream-name . "DepecheR")))
5843 (build-system r-build-system)
5845 `(("r-beanplot" ,r-beanplot)
5846 ("r-dosnow" ,r-dosnow)
5847 ("r-dplyr" ,r-dplyr)
5849 ("r-foreach" ,r-foreach)
5850 ("r-ggplot2" ,r-ggplot2)
5851 ("r-gplots" ,r-gplots)
5853 ("r-matrixstats" ,r-matrixstats)
5854 ("r-mixomics" ,r-mixomics)
5855 ("r-moments" ,r-moments)
5857 ("r-rcppeigen" ,r-rcppeigen)
5858 ("r-reshape2" ,r-reshape2)
5859 ("r-robustbase" ,r-robustbase)
5860 ("r-viridis" ,r-viridis)))
5861 (home-page "https://bioconductor.org/packages/DepecheR/")
5862 (synopsis "Identify traits of clusters in high-dimensional entities")
5864 "The purpose of this package is to identify traits in a dataset that can
5865 separate groups. This is done on two levels. First, clustering is performed,
5866 using an implementation of sparse K-means. Secondly, the generated clusters
5867 are used to predict outcomes of groups of individuals based on their
5868 distribution of observations in the different clusters. As certain clusters
5869 with separating information will be identified, and these clusters are defined
5870 by a sparse number of variables, this method can reduce the complexity of
5871 data, to only emphasize the data that actually matters.")
5872 (license license:expat)))
5874 (define-public r-rcistarget
5876 (name "r-rcistarget")
5881 (uri (bioconductor-uri "RcisTarget" version))
5884 "1nnah7s0jd24fpfyxsf76jas8dm23c3266aps124wdlqsp9q5qjw"))))
5885 (properties `((upstream-name . "RcisTarget")))
5886 (build-system r-build-system)
5888 `(("r-aucell" ,r-aucell)
5889 ("r-biocgenerics" ,r-biocgenerics)
5890 ("r-data-table" ,r-data-table)
5891 ("r-feather" ,r-feather)
5892 ("r-gseabase" ,r-gseabase)
5893 ("r-r-utils" ,r-r-utils)
5894 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5895 (home-page "https://aertslab.org/#scenic")
5896 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
5898 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
5899 over-represented on a gene list. In a first step, RcisTarget selects DNA
5900 motifs that are significantly over-represented in the surroundings of the
5901 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
5902 achieved by using a database that contains genome-wide cross-species rankings
5903 for each motif. The motifs that are then annotated to TFs and those that have
5904 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
5905 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
5906 genes in the gene-set that are ranked above the leading edge).")
5907 (license license:gpl3)))
5909 (define-public r-cicero
5916 (uri (bioconductor-uri "cicero" version))
5919 "0mmm7vvzq50b5fayid0bw82b5lar3xm9fwl2ya30q0p4db2y6wnz"))))
5920 (build-system r-build-system)
5922 `(("r-assertthat" ,r-assertthat)
5923 ("r-biobase" ,r-biobase)
5924 ("r-biocgenerics" ,r-biocgenerics)
5925 ("r-data-table" ,r-data-table)
5926 ("r-dplyr" ,r-dplyr)
5928 ("r-genomicranges" ,r-genomicranges)
5929 ("r-ggplot2" ,r-ggplot2)
5930 ("r-glasso" ,r-glasso)
5932 ("r-igraph" ,r-igraph)
5933 ("r-iranges" ,r-iranges)
5934 ("r-matrix" ,r-matrix)
5935 ("r-monocle" ,r-monocle)
5937 ("r-reshape2" ,r-reshape2)
5938 ("r-s4vectors" ,r-s4vectors)
5939 ("r-stringr" ,r-stringr)
5940 ("r-tibble" ,r-tibble)
5941 ("r-vgam" ,r-vgam)))
5942 (home-page "https://bioconductor.org/packages/cicero/")
5943 (synopsis "Predict cis-co-accessibility from single-cell data")
5945 "Cicero computes putative cis-regulatory maps from single-cell chromatin
5946 accessibility data. It also extends the monocle package for use in chromatin
5947 accessibility data.")
5948 (license license:expat)))
5950 ;; This is the latest commit on the "monocle3" branch.
5951 (define-public r-cicero-monocle3
5952 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
5954 (package (inherit r-cicero)
5955 (name "r-cicero-monocle3")
5956 (version (git-version "1.3.2" revision commit))
5961 (url "https://github.com/cole-trapnell-lab/cicero-release.git")
5963 (file-name (git-file-name name version))
5966 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
5968 `(("r-monocle3" ,r-monocle3)
5969 ,@(alist-delete "r-monocle"
5970 (package-propagated-inputs r-cicero)))))))
5972 (define-public r-cistopic
5973 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
5977 (version (git-version "0.2.1" revision commit))
5982 (url "https://github.com/aertslab/cisTopic.git")
5984 (file-name (git-file-name name version))
5987 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
5988 (build-system r-build-system)
5990 `(("r-aucell" ,r-aucell)
5991 ("r-data-table" ,r-data-table)
5992 ("r-dplyr" ,r-dplyr)
5993 ("r-dosnow" ,r-dosnow)
5995 ("r-feather" ,r-feather)
5996 ("r-fitdistrplus" ,r-fitdistrplus)
5997 ("r-genomicranges" ,r-genomicranges)
5998 ("r-ggplot2" ,r-ggplot2)
6000 ("r-matrix" ,r-matrix)
6002 ("r-rcistarget" ,r-rcistarget)
6003 ("r-rtracklayer" ,r-rtracklayer)
6004 ("r-s4vectors" ,r-s4vectors)))
6005 (home-page "https://github.com/aertslab/cisTopic")
6006 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
6008 "The sparse nature of single cell epigenomics data can be overruled using
6009 probabilistic modelling methods such as @dfn{Latent Dirichlet
6010 Allocation} (LDA). This package allows the probabilistic modelling of
6011 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
6012 includes functionalities to identify cell states based on the contribution of
6013 cisTopics and explore the nature and regulatory proteins driving them.")
6014 (license license:gpl3))))
6016 (define-public r-genie3
6023 (uri (bioconductor-uri "GENIE3" version))
6026 "0p67lhgy3lb4nc958s51hx7rvgwhzwfic9xhpsrask40k43spv7l"))))
6027 (properties `((upstream-name . "GENIE3")))
6028 (build-system r-build-system)
6029 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
6030 (home-page "https://bioconductor.org/packages/GENIE3")
6031 (synopsis "Gene network inference with ensemble of trees")
6033 "This package implements the GENIE3 algorithm for inferring gene
6034 regulatory networks from expression data.")
6035 (license license:gpl2+)))
6037 (define-public r-roc
6044 (uri (bioconductor-uri "ROC" version))
6047 "1aqpyc28czagg3nbybh55vf152nbar61jjw79w04326d97mc3j3y"))))
6048 (properties `((upstream-name . "ROC")))
6049 (build-system r-build-system)
6051 `(("r-knitr" ,r-knitr)))
6052 (home-page "https://www.bioconductor.org/packages/ROC/")
6053 (synopsis "Utilities for ROC curves")
6055 "This package provides utilities for @dfn{Receiver Operating
6056 Characteristic} (ROC) curves, with a focus on micro arrays.")
6057 (license license:artistic2.0)))
6059 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
6061 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
6066 (uri (bioconductor-uri
6067 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
6068 version 'annotation))
6071 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
6074 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
6075 (build-system r-build-system)
6076 (propagated-inputs `(("r-minfi" ,r-minfi)))
6078 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
6079 (synopsis "Annotation for Illumina's 450k methylation arrays")
6081 "This package provides manifests and annotation for Illumina's 450k array
6083 (license license:artistic2.0)))
6085 (define-public r-watermelon
6087 (name "r-watermelon")
6092 (uri (bioconductor-uri "wateRmelon" version))
6095 "0a66fq04yph9dis91lzjk9kh134zy6fj98yklrwf24r1080qngx0"))))
6096 (properties `((upstream-name . "wateRmelon")))
6097 (build-system r-build-system)
6099 `(("r-biobase" ,r-biobase)
6100 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
6101 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
6102 ("r-illuminaio" ,r-illuminaio)
6103 ("r-limma" ,r-limma)
6105 ("r-matrixstats" ,r-matrixstats)
6106 ("r-methylumi" ,r-methylumi)
6108 (home-page "https://bioconductor.org/packages/wateRmelon/")
6109 (synopsis "Illumina 450 methylation array normalization and metrics")
6111 "The standard index of DNA methylation (beta) is computed from methylated
6112 and unmethylated signal intensities. Betas calculated from raw signal
6113 intensities perform well, but using 11 methylomic datasets we demonstrate that
6114 quantile normalization methods produce marked improvement. The commonly used
6115 procedure of normalizing betas is inferior to the separate normalization of M
6116 and U, and it is also advantageous to normalize Type I and Type II assays
6117 separately. This package provides 15 flavours of betas and three performance
6118 metrics, with methods for objects produced by the @code{methylumi} and
6119 @code{minfi} packages.")
6120 (license license:gpl3)))
6122 (define-public r-gdsfmt
6129 (uri (bioconductor-uri "gdsfmt" version))
6132 "0zc9v62imd0ykz4h30pxa64q0y45qijmkwdk2pd4ncsg8fc2jlz9"))
6133 (modules '((guix build utils)))
6134 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
6135 ;; them and link with system libraries instead.
6138 (for-each delete-file-recursively
6142 (substitute* "src/Makevars"
6143 (("all: \\$\\(SHLIB\\)") "all:")
6144 (("\\$\\(SHLIB\\): liblzma.a") "")
6145 (("(ZLIB|LZ4)/.*") "")
6146 (("CoreArray/dVLIntGDS.cpp.*")
6147 "CoreArray/dVLIntGDS.cpp")
6148 (("CoreArray/dVLIntGDS.o.*")
6149 "CoreArray/dVLIntGDS.o")
6150 (("PKG_LIBS = ./liblzma.a")
6151 "PKG_LIBS = -llz4"))
6152 (substitute* "src/CoreArray/dStream.h"
6153 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
6154 (string-append "include <" header ">")))
6156 (properties `((upstream-name . "gdsfmt")))
6157 (build-system r-build-system)
6162 (home-page "http://corearray.sourceforge.net/")
6164 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
6166 "This package provides a high-level R interface to CoreArray @dfn{Genomic
6167 Data Structure} (GDS) data files, which are portable across platforms with
6168 hierarchical structure to store multiple scalable array-oriented data sets
6169 with metadata information. It is suited for large-scale datasets, especially
6170 for data which are much larger than the available random-access memory. The
6171 @code{gdsfmt} package offers efficient operations specifically designed for
6172 integers of less than 8 bits, since a diploid genotype, like
6173 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
6174 byte. Data compression and decompression are available with relatively
6175 efficient random access. It is also allowed to read a GDS file in parallel
6176 with multiple R processes supported by the package @code{parallel}.")
6177 (license license:lgpl3)))
6179 (define-public r-bigmelon
6186 (uri (bioconductor-uri "bigmelon" version))
6189 "0sw7rp4p03m1s72b4j06jfb7as3v1n2w2z4ppk8s4f80fb05bcls"))))
6190 (properties `((upstream-name . "bigmelon")))
6191 (build-system r-build-system)
6193 `(("r-biobase" ,r-biobase)
6194 ("r-biocgenerics" ,r-biocgenerics)
6195 ("r-gdsfmt" ,r-gdsfmt)
6196 ("r-geoquery" ,r-geoquery)
6197 ("r-methylumi" ,r-methylumi)
6198 ("r-minfi" ,r-minfi)
6199 ("r-watermelon" ,r-watermelon)))
6200 (home-page "https://bioconductor.org/packages/bigmelon/")
6201 (synopsis "Illumina methylation array analysis for large experiments")
6203 "This package provides methods for working with Illumina arrays using the
6204 @code{gdsfmt} package.")
6205 (license license:gpl3)))
6207 (define-public r-seqbias
6214 (uri (bioconductor-uri "seqbias" version))
6217 "19vbdyjblij2533ibmrw1n0rkqfrbflma6cg5b79ghks0mg7z8hq"))))
6218 (properties `((upstream-name . "seqbias")))
6219 (build-system r-build-system)
6221 `(("r-biostrings" ,r-biostrings)
6222 ("r-genomicranges" ,r-genomicranges)
6223 ("r-rhtslib" ,r-rhtslib)))
6225 `(("zlib" ,zlib))) ; This comes from rhtslib.
6226 (home-page "https://bioconductor.org/packages/seqbias/")
6227 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
6229 "This package implements a model of per-position sequencing bias in
6230 high-throughput sequencing data using a simple Bayesian network, the structure
6231 and parameters of which are trained on a set of aligned reads and a reference
6233 (license license:lgpl3)))
6235 (define-public r-reqon
6242 (uri (bioconductor-uri "ReQON" version))
6245 "10p6l2zxijqyypdm970jyfqyrnfhaq3nf7cg2q6mgd1srggfa0cx"))))
6246 (properties `((upstream-name . "ReQON")))
6247 (build-system r-build-system)
6249 `(("r-rjava" ,r-rjava)
6250 ("r-rsamtools" ,r-rsamtools)
6251 ("r-seqbias" ,r-seqbias)))
6252 (home-page "https://bioconductor.org/packages/ReQON/")
6253 (synopsis "Recalibrating quality of nucleotides")
6255 "This package provides an implementation of an algorithm for
6256 recalibrating the base quality scores for aligned sequencing data in BAM
6258 (license license:gpl2)))
6260 (define-public r-wavcluster
6262 (name "r-wavcluster")
6267 (uri (bioconductor-uri "wavClusteR" version))
6270 "0vq3xxsvwq86rlya7xc92sc4i6b48sib0pcina3xivg3ky2j3z7y"))))
6271 (properties `((upstream-name . "wavClusteR")))
6272 (build-system r-build-system)
6274 `(("r-biocgenerics" ,r-biocgenerics)
6275 ("r-biostrings" ,r-biostrings)
6276 ("r-foreach" ,r-foreach)
6277 ("r-genomicfeatures" ,r-genomicfeatures)
6278 ("r-genomicranges" ,r-genomicranges)
6279 ("r-ggplot2" ,r-ggplot2)
6280 ("r-hmisc" ,r-hmisc)
6281 ("r-iranges" ,r-iranges)
6282 ("r-mclust" ,r-mclust)
6283 ("r-rsamtools" ,r-rsamtools)
6284 ("r-rtracklayer" ,r-rtracklayer)
6285 ("r-s4vectors" ,r-s4vectors)
6286 ("r-seqinr" ,r-seqinr)
6287 ("r-stringr" ,r-stringr)
6288 ("r-wmtsa" ,r-wmtsa)))
6289 (home-page "https://bioconductor.org/packages/wavClusteR/")
6290 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
6292 "This package provides an integrated pipeline for the analysis of
6293 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
6294 sequencing errors, SNPs and additional non-experimental sources by a non-
6295 parametric mixture model. The protein binding sites (clusters) are then
6296 resolved at high resolution and cluster statistics are estimated using a
6297 rigorous Bayesian framework. Post-processing of the results, data export for
6298 UCSC genome browser visualization and motif search analysis are provided. In
6299 addition, the package allows to integrate RNA-Seq data to estimate the False
6300 Discovery Rate of cluster detection. Key functions support parallel multicore
6301 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
6302 be applied to the analysis of other NGS data obtained from experimental
6303 procedures that induce nucleotide substitutions (e.g. BisSeq).")
6304 (license license:gpl2)))
6306 (define-public r-timeseriesexperiment
6308 (name "r-timeseriesexperiment")
6313 (uri (bioconductor-uri "TimeSeriesExperiment" version))
6316 "0xqa6hzknnci20zx2f6mw5cpqx8pq0v6fzf053hh51p1l2ikvgqm"))))
6318 `((upstream-name . "TimeSeriesExperiment")))
6319 (build-system r-build-system)
6321 `(("r-deseq2" ,r-deseq2)
6322 ("r-dplyr" ,r-dplyr)
6323 ("r-dynamictreecut" ,r-dynamictreecut)
6324 ("r-edger" ,r-edger)
6325 ("r-ggplot2" ,r-ggplot2)
6326 ("r-hmisc" ,r-hmisc)
6327 ("r-limma" ,r-limma)
6328 ("r-magrittr" ,r-magrittr)
6329 ("r-proxy" ,r-proxy)
6330 ("r-s4vectors" ,r-s4vectors)
6331 ("r-summarizedexperiment" ,r-summarizedexperiment)
6332 ("r-tibble" ,r-tibble)
6333 ("r-tidyr" ,r-tidyr)
6334 ("r-vegan" ,r-vegan)
6335 ("r-viridis" ,r-viridis)))
6336 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
6337 (synopsis "Analysis for short time-series data")
6339 "This package is a visualization and analysis toolbox for short time
6340 course data which includes dimensionality reduction, clustering, two-sample
6341 differential expression testing and gene ranking techniques. The package also
6342 provides methods for retrieving enriched pathways.")
6343 (license license:lgpl3+)))
6345 (define-public r-variantfiltering
6347 (name "r-variantfiltering")
6352 (uri (bioconductor-uri "VariantFiltering" version))
6355 "13pgfk2mbffd9smmxnwz7g0jrwng78711053wfzadr107zbyn4r8"))))
6357 `((upstream-name . "VariantFiltering")))
6358 (build-system r-build-system)
6360 `(("r-annotationdbi" ,r-annotationdbi)
6361 ("r-biobase" ,r-biobase)
6362 ("r-biocgenerics" ,r-biocgenerics)
6363 ("r-biocparallel" ,r-biocparallel)
6364 ("r-biostrings" ,r-biostrings)
6365 ("r-bsgenome" ,r-bsgenome)
6367 ("r-genomeinfodb" ,r-genomeinfodb)
6368 ("r-genomicfeatures" ,r-genomicfeatures)
6369 ("r-genomicranges" ,r-genomicranges)
6370 ("r-genomicscores" ,r-genomicscores)
6371 ("r-graph" ,r-graph)
6373 ("r-iranges" ,r-iranges)
6375 ("r-rsamtools" ,r-rsamtools)
6376 ("r-s4vectors" ,r-s4vectors)
6377 ("r-shiny" ,r-shiny)
6378 ("r-shinyjs" ,r-shinyjs)
6379 ("r-shinythemes" ,r-shinythemes)
6380 ("r-shinytree" ,r-shinytree)
6381 ("r-summarizedexperiment" ,r-summarizedexperiment)
6382 ("r-variantannotation" ,r-variantannotation)
6383 ("r-xvector" ,r-xvector)))
6384 (home-page "https://github.com/rcastelo/VariantFiltering")
6385 (synopsis "Filtering of coding and non-coding genetic variants")
6387 "Filter genetic variants using different criteria such as inheritance
6388 model, amino acid change consequence, minor allele frequencies across human
6389 populations, splice site strength, conservation, etc.")
6390 (license license:artistic2.0)))
6392 (define-public r-genomegraphs
6394 (name "r-genomegraphs")
6399 (uri (bioconductor-uri "GenomeGraphs" version))
6402 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
6403 (properties `((upstream-name . "GenomeGraphs")))
6404 (build-system r-build-system)
6406 `(("r-biomart" ,r-biomart)))
6407 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
6408 (synopsis "Plotting genomic information from Ensembl")
6410 "Genomic data analyses requires integrated visualization of known genomic
6411 information and new experimental data. GenomeGraphs uses the biomaRt package
6412 to perform live annotation queries to Ensembl and translates this to e.g.
6413 gene/transcript structures in viewports of the grid graphics package. This
6414 results in genomic information plotted together with your data. Another
6415 strength of GenomeGraphs is to plot different data types such as array CGH,
6416 gene expression, sequencing and other data, together in one plot using the
6417 same genome coordinate system.")
6418 (license license:artistic2.0)))
6420 (define-public r-wavetiling
6422 (name "r-wavetiling")
6427 (uri (bioconductor-uri "waveTiling" version))
6430 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
6431 (properties `((upstream-name . "waveTiling")))
6432 (build-system r-build-system)
6434 `(("r-affy" ,r-affy)
6435 ("r-biobase" ,r-biobase)
6436 ("r-biostrings" ,r-biostrings)
6437 ("r-genomegraphs" ,r-genomegraphs)
6438 ("r-genomicranges" ,r-genomicranges)
6439 ("r-iranges" ,r-iranges)
6440 ("r-oligo" ,r-oligo)
6441 ("r-oligoclasses" ,r-oligoclasses)
6442 ("r-preprocesscore" ,r-preprocesscore)
6443 ("r-waveslim" ,r-waveslim)))
6444 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
6445 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
6447 "This package is designed to conduct transcriptome analysis for tiling
6448 arrays based on fast wavelet-based functional models.")
6449 (license license:gpl2+)))
6451 (define-public r-variancepartition
6453 (name "r-variancepartition")
6458 (uri (bioconductor-uri "variancePartition" version))
6461 "1ygx7f2sp4b7ilgspm6vqcbjxs7br9s6g3gwcdb978kx03ymp4i8"))))
6463 `((upstream-name . "variancePartition")))
6464 (build-system r-build-system)
6466 `(("r-biobase" ,r-biobase)
6467 ("r-biocparallel" ,r-biocparallel)
6468 ("r-colorramps" ,r-colorramps)
6469 ("r-doparallel" ,r-doparallel)
6470 ("r-foreach" ,r-foreach)
6471 ("r-ggplot2" ,r-ggplot2)
6472 ("r-gplots" ,r-gplots)
6473 ("r-iterators" ,r-iterators)
6474 ("r-limma" ,r-limma)
6476 ("r-lmertest" ,r-lmertest)
6478 ("r-pbkrtest" ,r-pbkrtest)
6479 ("r-progress" ,r-progress)
6480 ("r-reshape2" ,r-reshape2)
6481 ("r-scales" ,r-scales)))
6482 (home-page "https://bioconductor.org/packages/variancePartition/")
6483 (synopsis "Analyze variation in gene expression experiments")
6485 "This is a package providing tools to quantify and interpret multiple
6486 sources of biological and technical variation in gene expression experiments.
6487 It uses a linear mixed model to quantify variation in gene expression
6488 attributable to individual, tissue, time point, or technical variables. The
6489 package includes dream differential expression analysis for repeated
6491 (license license:gpl2+)))
6493 (define-public r-htqpcr
6500 (uri (bioconductor-uri "HTqPCR" version))
6503 "008iczqaa0wn5nw144vfg3qylg7qa1q963nq9mqhgj3sxlg4rmjx"))))
6504 (properties `((upstream-name . "HTqPCR")))
6505 (build-system r-build-system)
6507 `(("r-affy" ,r-affy)
6508 ("r-biobase" ,r-biobase)
6509 ("r-gplots" ,r-gplots)
6510 ("r-limma" ,r-limma)
6511 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6512 (home-page "http://www.ebi.ac.uk/bertone/software")
6513 (synopsis "Automated analysis of high-throughput qPCR data")
6515 "Analysis of Ct values from high throughput quantitative real-time
6516 PCR (qPCR) assays across multiple conditions or replicates. The input data
6517 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
6518 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
6519 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
6520 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
6521 loading, quality assessment, normalization, visualization and parametric or
6522 non-parametric testing for statistical significance in Ct values between
6523 features (e.g. genes, microRNAs).")
6524 (license license:artistic2.0)))
6526 (define-public r-unifiedwmwqpcr
6528 (name "r-unifiedwmwqpcr")
6533 (uri (bioconductor-uri "unifiedWMWqPCR" version))
6536 "1l6rf7scxxyz4x0m4li54y6905sqj4jrx481zb9h3vqhcfcmn8lj"))))
6538 `((upstream-name . "unifiedWMWqPCR")))
6539 (build-system r-build-system)
6541 `(("r-biocgenerics" ,r-biocgenerics)
6542 ("r-htqpcr" ,r-htqpcr)))
6543 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
6544 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
6546 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
6547 data. This modified test allows for testing differential expression in qPCR
6549 (license license:gpl2+)))
6551 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
6553 (define-public r-activedriverwgs
6555 (name "r-activedriverwgs")
6560 (uri (cran-uri "ActiveDriverWGS" version))
6563 "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1"))))
6565 `((upstream-name . "ActiveDriverWGS")))
6566 (build-system r-build-system)
6568 `(("r-biostrings" ,r-biostrings)
6569 ("r-bsgenome" ,r-bsgenome)
6570 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
6571 ("r-genomeinfodb" ,r-genomeinfodb)
6572 ("r-genomicranges" ,r-genomicranges)
6573 ("r-iranges" ,r-iranges)
6575 ("r-s4vectors" ,r-s4vectors)))
6576 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
6577 (synopsis "Driver discovery tool for cancer whole genomes")
6579 "This package provides a method for finding an enrichment of cancer
6580 simple somatic mutations (SNVs and Indels) in functional elements across the
6581 human genome. ActiveDriverWGS detects coding and noncoding driver elements
6582 using whole genome sequencing data.")
6583 (license license:gpl3)))
6585 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
6587 (define-public r-activepathways
6589 (name "r-activepathways")
6594 (uri (cran-uri "ActivePathways" version))
6597 "1xb0d1svmzw404pv8ja6wr4773k7x2lxkrzrayilvzqbfzj1wx20"))))
6599 `((upstream-name . "ActivePathways")))
6600 (build-system r-build-system)
6602 `(("r-data-table" ,r-data-table)
6603 ("r-ggplot2" ,r-ggplot2)
6604 ("r-metap" ,r-metap)))
6605 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
6606 (synopsis "Multivariate pathway enrichment analysis")
6608 "This package represents an integrative method of analyzing multi omics
6609 data that conducts enrichment analysis of annotated gene sets. ActivePathways
6610 uses a statistical data fusion approach, rationalizes contributing evidence
6611 and highlights associated genes, improving systems-level understanding of
6612 cellular organization in health and disease.")
6613 (license license:gpl3)))
6615 (define-public r-bgmix
6622 (uri (bioconductor-uri "BGmix" version))
6625 "1bwqqhkh4m3hhpd71grwjrg7n07lzvys4y7aghmw2gw5ibnk5683"))))
6626 (properties `((upstream-name . "BGmix")))
6627 (build-system r-build-system)
6629 `(("r-kernsmooth" ,r-kernsmooth)))
6630 (home-page "https://bioconductor.org/packages/BGmix/")
6631 (synopsis "Bayesian models for differential gene expression")
6633 "This package provides fully Bayesian mixture models for differential
6635 (license license:gpl2)))
6637 (define-public r-bgx
6644 (uri (bioconductor-uri "bgx" version))
6647 "0fiqqv6pin0zhxaw67hzfjccq2qkl9qfqjf10nx2zmpxm2licavm"))))
6648 (properties `((upstream-name . "bgx")))
6649 (build-system r-build-system)
6651 `(("r-affy" ,r-affy)
6652 ("r-biobase" ,r-biobase)
6653 ("r-gcrma" ,r-gcrma)
6654 ("r-rcpp" ,r-rcpp)))
6655 (home-page "https://bioconductor.org/packages/bgx/")
6656 (synopsis "Bayesian gene expression")
6658 "This package provides tools for Bayesian integrated analysis of
6659 Affymetrix GeneChips.")
6660 (license license:gpl2)))
6662 (define-public r-bhc
6669 (uri (bioconductor-uri "BHC" version))
6672 "1bxx3jak8mgvay3j1xd59bb9j86pzl6hh5abxww9x1b7rswmy1jh"))))
6673 (properties `((upstream-name . "BHC")))
6674 (build-system r-build-system)
6675 (home-page "https://bioconductor.org/packages/BHC/")
6676 (synopsis "Bayesian hierarchical clustering")
6678 "The method implemented in this package performs bottom-up hierarchical
6679 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
6680 in the data and Bayesian model selection to decide at each step which clusters
6681 to merge. This avoids several limitations of traditional methods, for example
6682 how many clusters there should be and how to choose a principled distance
6683 metric. This implementation accepts multinomial (i.e. discrete, with 2+
6684 categories) or time-series data. This version also includes a randomised
6685 algorithm which is more efficient for larger data sets.")
6686 (license license:gpl3)))
6688 (define-public r-bicare
6695 (uri (bioconductor-uri "BicARE" version))
6698 "1gia5vzmvbk4k1vx3bh9nld1ws9s3c0y11qfbzqhfnfjbd7n8qcs"))))
6699 (properties `((upstream-name . "BicARE")))
6700 (build-system r-build-system)
6702 `(("r-biobase" ,r-biobase)
6703 ("r-gseabase" ,r-gseabase)
6704 ("r-multtest" ,r-multtest)))
6705 (home-page "http://bioinfo.curie.fr")
6706 (synopsis "Biclustering analysis and results exploration")
6708 "This is a package for biclustering analysis and exploration of
6710 (license license:gpl2)))
6712 (define-public r-bifet
6719 (uri (bioconductor-uri "BiFET" version))
6722 "0ck1d6hxd4f40hfz8p2z5xmjbz79yhrf6fisjka2xzk5v9fm4p4k"))))
6723 (properties `((upstream-name . "BiFET")))
6724 (build-system r-build-system)
6726 `(("r-genomicranges" ,r-genomicranges)
6727 ("r-poibin" ,r-poibin)))
6728 (home-page "https://bioconductor.org/packages/BiFET")
6729 (synopsis "Bias-free footprint enrichment test")
6731 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
6732 over-represented in target regions compared to background regions after
6733 correcting for the bias arising from the imbalance in read counts and GC
6734 contents between the target and background regions. For a given TF k, BiFET
6735 tests the null hypothesis that the target regions have the same probability of
6736 having footprints for the TF k as the background regions while correcting for
6737 the read count and GC content bias.")
6738 (license license:gpl3)))
6740 (define-public r-rsbml
6747 (uri (bioconductor-uri "rsbml" version))
6750 "1dbp0aaijxn3na26b68ws0v9qzvml61ifb9z4i8pz7q6h48n7lxa"))))
6751 (properties `((upstream-name . "rsbml")))
6752 (build-system r-build-system)
6754 `(("libsbml" ,libsbml)
6757 `(("r-biocgenerics" ,r-biocgenerics)
6758 ("r-graph" ,r-graph)))
6760 `(("pkg-config" ,pkg-config)))
6761 (home-page "http://www.sbml.org")
6762 (synopsis "R support for SBML")
6764 "This package provides an R interface to libsbml for SBML parsing,
6765 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
6766 (license license:artistic2.0)))
6768 (define-public r-hypergraph
6770 (name "r-hypergraph")
6775 (uri (bioconductor-uri "hypergraph" version))
6778 "1bixmslxy7r987zw1vf4dg72hfi04lf4vj03n7ygym2g8nfhbh7m"))))
6779 (properties `((upstream-name . "hypergraph")))
6780 (build-system r-build-system)
6782 `(("r-graph" ,r-graph)))
6783 (home-page "https://bioconductor.org/packages/hypergraph")
6784 (synopsis "Hypergraph data structures")
6786 "This package implements some simple capabilities for representing and
6787 manipulating hypergraphs.")
6788 (license license:artistic2.0)))
6790 (define-public r-hyperdraw
6792 (name "r-hyperdraw")
6797 (uri (bioconductor-uri "hyperdraw" version))
6800 "0a8h3pb7196qi49ady8ni92m5wqb1hvxw6khk9j63mwj3h7jinbj"))))
6801 (properties `((upstream-name . "hyperdraw")))
6802 (build-system r-build-system)
6803 (inputs `(("graphviz" ,graphviz)))
6805 `(("r-graph" ,r-graph)
6806 ("r-hypergraph" ,r-hypergraph)
6807 ("r-rgraphviz" ,r-rgraphviz)))
6808 (home-page "https://bioconductor.org/packages/hyperdraw")
6809 (synopsis "Visualizing hypergraphs")
6811 "This package provides functions for visualizing hypergraphs.")
6812 (license license:gpl2+)))
6814 (define-public r-biggr
6821 (uri (bioconductor-uri "BiGGR" version))
6824 "1n2ypc84abmhn6br0yi87k7lvjc11k7abzhgvzdabc2ai1qgcqif"))))
6825 (properties `((upstream-name . "BiGGR")))
6826 (build-system r-build-system)
6828 `(("r-hyperdraw" ,r-hyperdraw)
6829 ("r-hypergraph" ,r-hypergraph)
6831 ("r-limsolve" ,r-limsolve)
6832 ("r-rsbml" ,r-rsbml)
6833 ("r-stringr" ,r-stringr)))
6834 (home-page "https://bioconductor.org/packages/BiGGR/")
6835 (synopsis "Constraint based modeling using metabolic reconstruction databases")
6837 "This package provides an interface to simulate metabolic reconstruction
6838 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
6839 reconstruction databases. The package facilitates @dfn{flux balance
6840 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
6841 networks and estimated fluxes can be visualized with hypergraphs.")
6842 (license license:gpl3+)))
6844 (define-public r-bigmemoryextras
6846 (name "r-bigmemoryextras")
6851 (uri (bioconductor-uri "bigmemoryExtras" version))
6854 "17dk7c44ikphcrpi8hnxyvlmj30qmj098kc0ihfi69bp9rw1cibq"))))
6856 `((upstream-name . "bigmemoryExtras")))
6857 (build-system r-build-system)
6859 `(("r-bigmemory" ,r-bigmemory)))
6860 (home-page "https://github.com/phaverty/bigmemoryExtras")
6861 (synopsis "Extension of the bigmemory package")
6863 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
6864 safety and convenience features to the @code{filebacked.big.matrix} class from
6865 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
6866 monitoring and gracefully restoring the connection to on-disk data and it also
6867 protects against accidental data modification with a filesystem-based
6868 permissions system. Utilities are provided for using @code{BigMatrix}-derived
6869 classes as @code{assayData} matrices within the @code{Biobase} package's
6870 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
6871 related to attaching to, and indexing into, file-backed matrices with
6872 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
6873 a file-backed matrix with factor properties.")
6874 (license license:artistic2.0)))
6876 (define-public r-bigpint
6883 (uri (bioconductor-uri "bigPint" version))
6886 "10vs0lzfyxp6sm4r9pxfwipjvzmmaqnvwn1hc5q37s5qz44fg0hk"))))
6887 (properties `((upstream-name . "bigPint")))
6888 (build-system r-build-system)
6890 `(("r-dplyr" ,r-dplyr)
6891 ("r-ggally" ,r-ggally)
6892 ("r-ggplot2" ,r-ggplot2)
6893 ("r-gridextra" ,r-gridextra)
6894 ("r-hexbin" ,r-hexbin)
6895 ("r-hmisc" ,r-hmisc)
6896 ("r-htmlwidgets" ,r-htmlwidgets)
6897 ("r-plotly" ,r-plotly)
6899 ("r-rcolorbrewer" ,r-rcolorbrewer)
6900 ("r-reshape" ,r-reshape)
6901 ("r-shiny" ,r-shiny)
6902 ("r-shinycssloaders" ,r-shinycssloaders)
6903 ("r-shinydashboard" ,r-shinydashboard)
6904 ("r-stringr" ,r-stringr)
6905 ("r-tidyr" ,r-tidyr)))
6906 (home-page "https://github.com/lindsayrutter/bigPint")
6907 (synopsis "Big multivariate data plotted interactively")
6909 "This package provides methods for visualizing large multivariate
6910 datasets using static and interactive scatterplot matrices, parallel
6911 coordinate plots, volcano plots, and litre plots. It includes examples for
6912 visualizing RNA-sequencing datasets and differentially expressed genes.")
6913 (license license:gpl3)))
6915 (define-public r-chemminer
6917 (name "r-chemminer")
6922 (uri (bioconductor-uri "ChemmineR" version))
6925 "1j6vmkhc03dmmkm5wgbcv62pw5dclp49f906xkx1pwg27bdldbga"))))
6926 (properties `((upstream-name . "ChemmineR")))
6927 (build-system r-build-system)
6929 `(("r-base64enc" ,r-base64enc)
6931 ("r-biocgenerics" ,r-biocgenerics)
6933 ("r-digest" ,r-digest)
6935 ("r-ggplot2" ,r-ggplot2)
6936 ("r-gridextra" ,r-gridextra)
6939 ("r-rcurl" ,r-rcurl)
6940 ("r-rjson" ,r-rjson)
6941 ("r-rsvg" ,r-rsvg)))
6942 (home-page "https://github.com/girke-lab/ChemmineR")
6943 (synopsis "Cheminformatics toolkit for R")
6945 "ChemmineR is a cheminformatics package for analyzing drug-like small
6946 molecule data in R. It contains functions for efficient processing of large
6947 numbers of molecules, physicochemical/structural property predictions,
6948 structural similarity searching, classification and clustering of compound
6949 libraries with a wide spectrum of algorithms. In addition, it offers
6950 visualization functions for compound clustering results and chemical
6952 (license license:artistic2.0)))
6954 (define-public r-bioassayr
6956 (name "r-bioassayr")
6961 (uri (bioconductor-uri "bioassayR" version))
6964 "08vxkvxhqnryfbj4dwk3ifb9pn544www9zk2pj9fjbh5xfpwi7zw"))))
6965 (properties `((upstream-name . "bioassayR")))
6966 (build-system r-build-system)
6968 `(("r-biocgenerics" ,r-biocgenerics)
6969 ("r-chemminer" ,r-chemminer)
6971 ("r-matrix" ,r-matrix)
6972 ("r-rjson" ,r-rjson)
6973 ("r-rsqlite" ,r-rsqlite)
6975 (home-page "https://github.com/TylerBackman/bioassayR")
6976 (synopsis "Cross-target analysis of small molecule bioactivity")
6978 "bioassayR is a computational tool that enables simultaneous analysis of
6979 thousands of bioassay experiments performed over a diverse set of compounds
6980 and biological targets. Unique features include support for large-scale
6981 cross-target analyses of both public and custom bioassays, generation of
6982 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
6983 preloaded database that provides access to a substantial portion of publicly
6984 available bioactivity data.")
6985 (license license:artistic2.0)))
6987 (define-public r-biobroom
6994 (uri (bioconductor-uri "biobroom" version))
6997 "1480ycdsh9xdhbpr47vdw5g6m8arqsnp8hc19wwhzm8npxh4qqlb"))))
6998 (properties `((upstream-name . "biobroom")))
6999 (build-system r-build-system)
7001 `(("r-biobase" ,r-biobase)
7002 ("r-broom" ,r-broom)
7003 ("r-dplyr" ,r-dplyr)
7004 ("r-tidyr" ,r-tidyr)))
7005 (home-page "https://github.com/StoreyLab/biobroom")
7006 (synopsis "Turn Bioconductor objects into tidy data frames")
7008 "This package contains methods for converting standard objects
7009 constructed by bioinformatics packages, especially those in Bioconductor, and
7010 converting them to @code{tidy} data. It thus serves as a complement to the
7011 @code{broom} package, and follows the same tidy, augment, glance division of
7012 tidying methods. Tidying data makes it easy to recombine, reshape and
7013 visualize bioinformatics analyses.")
7014 ;; Any version of the LGPL.
7015 (license license:lgpl3+)))
7017 (define-public r-graphite
7024 (uri (bioconductor-uri "graphite" version))
7027 "1r9fk0cpdwm7012pa85dkjcpkml2j89zcznpf4hfdz66anfyyycd"))))
7028 (properties `((upstream-name . "graphite")))
7029 (build-system r-build-system)
7031 `(("r-annotationdbi" ,r-annotationdbi)
7032 ("r-checkmate" ,r-checkmate)
7033 ("r-graph" ,r-graph)
7035 ("r-rappdirs" ,r-rappdirs)))
7036 (home-page "https://bioconductor.org/packages/graphite/")
7037 (synopsis "Networks from pathway databases")
7039 "Graphite provides networks derived from eight public pathway databases,
7040 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
7042 (license license:agpl3+)))
7044 (define-public r-reactomepa
7046 (name "r-reactomepa")
7051 (uri (bioconductor-uri "ReactomePA" version))
7054 "1vwc9kj1l4yi7c4f4lnq0i3wl2nrmmhcxyakz8qak122fi92z3j1"))))
7055 (properties `((upstream-name . "ReactomePA")))
7056 (build-system r-build-system)
7058 `(("r-annotationdbi" ,r-annotationdbi)
7060 ("r-enrichplot" ,r-enrichplot)
7061 ("r-ggplot2" ,r-ggplot2)
7062 ("r-ggraph" ,r-ggraph)
7063 ("r-graphite" ,r-graphite)
7064 ("r-igraph" ,r-igraph)
7065 ("r-reactome-db" ,r-reactome-db)))
7066 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
7067 (synopsis "Reactome pathway analysis")
7069 "This package provides functions for pathway analysis based on the
7070 REACTOME pathway database. It implements enrichment analysis, gene set
7071 enrichment analysis and several functions for visualization.")
7072 (license license:gpl2)))
7074 (define-public r-ebarrays
7081 (uri (bioconductor-uri "EBarrays" version))
7084 "063rhsdp8x0f881kslq06zxfp6b2qabrz4vmfrn8a4v3pd3n7s13"))))
7085 (properties `((upstream-name . "EBarrays")))
7086 (build-system r-build-system)
7088 `(("r-biobase" ,r-biobase)
7089 ("r-cluster" ,r-cluster)
7090 ("r-lattice" ,r-lattice)))
7091 (home-page "https://bioconductor.org/packages/EBarrays/")
7092 (synopsis "Gene clustering and differential expression identification")
7094 "EBarrays provides tools for the analysis of replicated/unreplicated
7096 (license license:gpl2+)))
7098 (define-public r-bioccasestudies
7100 (name "r-bioccasestudies")
7105 (uri (bioconductor-uri "BiocCaseStudies" version))
7108 "1sg9vxs24zfz3dg9y0qlrdsq43y0pbahbvcfxzlxjzjw80xzxpbd"))))
7110 `((upstream-name . "BiocCaseStudies")))
7111 (build-system r-build-system)
7112 (propagated-inputs `(("r-biobase" ,r-biobase)))
7113 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
7114 (synopsis "Support for the case studies monograph")
7116 "This package provides software and data to support the case studies
7118 (license license:artistic2.0)))
7120 (define-public r-biocgraph
7122 (name "r-biocgraph")
7127 (uri (bioconductor-uri "biocGraph" version))
7130 "1rv2lwiqwg7h7za23n896fs4dpla3xhw6kzwghb6iw5nlm2m61yw"))))
7131 (properties `((upstream-name . "biocGraph")))
7132 (build-system r-build-system)
7134 `(("r-biocgenerics" ,r-biocgenerics)
7135 ("r-geneplotter" ,r-geneplotter)
7136 ("r-graph" ,r-graph)
7137 ("r-rgraphviz" ,r-rgraphviz)))
7138 (home-page "https://bioconductor.org/packages/biocGraph/")
7139 (synopsis "Graph examples and use cases in Bioinformatics")
7141 "This package provides examples and code that make use of the
7142 different graph related packages produced by Bioconductor.")
7143 (license license:artistic2.0)))
7145 (define-public r-experimenthub
7147 (name "r-experimenthub")
7152 (uri (bioconductor-uri "ExperimentHub" version))
7155 "054w2lkyirbmhgia0rp4nk9zzw3zphz6jxg6fc9zlarp90g64z24"))))
7156 (properties `((upstream-name . "ExperimentHub")))
7157 (build-system r-build-system)
7159 `(("r-annotationhub" ,r-annotationhub)
7160 ("r-biocfilecache" ,r-biocfilecache)
7161 ("r-biocgenerics" ,r-biocgenerics)
7162 ("r-biocmanager" ,r-biocmanager)
7164 ("r-rappdirs" ,r-rappdirs)
7165 ("r-s4vectors" ,r-s4vectors)))
7166 (home-page "https://bioconductor.org/packages/ExperimentHub/")
7167 (synopsis "Client to access ExperimentHub resources")
7169 "This package provides a client for the Bioconductor ExperimentHub web
7170 resource. ExperimentHub provides a central location where curated data from
7171 experiments, publications or training courses can be accessed. Each resource
7172 has associated metadata, tags and date of modification. The client creates
7173 and manages a local cache of files retrieved enabling quick and reproducible
7175 (license license:artistic2.0)))
7177 (define-public r-multiassayexperiment
7179 (name "r-multiassayexperiment")
7184 (uri (bioconductor-uri "MultiAssayExperiment" version))
7187 "0xpi5qpffg9pn8szkvicpc43a0r534wngyqwvsip8w66zi8c9kpc"))))
7189 `((upstream-name . "MultiAssayExperiment")))
7190 (build-system r-build-system)
7192 `(("r-biobase" ,r-biobase)
7193 ("r-biocgenerics" ,r-biocgenerics)
7194 ("r-genomicranges" ,r-genomicranges)
7195 ("r-iranges" ,r-iranges)
7196 ("r-s4vectors" ,r-s4vectors)
7197 ("r-summarizedexperiment" ,r-summarizedexperiment)
7198 ("r-tidyr" ,r-tidyr)))
7199 (home-page "http://waldronlab.io/MultiAssayExperiment/")
7200 (synopsis "Integration of multi-omics experiments in Bioconductor")
7202 "MultiAssayExperiment harmonizes data management of multiple assays
7203 performed on an overlapping set of specimens. It provides a familiar
7204 Bioconductor user experience by extending concepts from
7205 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
7206 classes for individual assays, and allowing subsetting by genomic ranges or
7208 (license license:artistic2.0)))
7210 (define-public r-bioconcotk
7212 (name "r-bioconcotk")
7217 (uri (bioconductor-uri "BiocOncoTK" version))
7220 "0rnah6c01a33yb9663jim9iclan61rpcwprb56mykgn1pf5hywbj"))))
7221 (properties `((upstream-name . "BiocOncoTK")))
7222 (build-system r-build-system)
7224 `(("r-bigrquery" ,r-bigrquery)
7226 ("r-complexheatmap" ,r-complexheatmap)
7227 ("r-curatedtcgadata" ,r-curatedtcgadata)
7229 ("r-dplyr" ,r-dplyr)
7231 ("r-genomicfeatures" ,r-genomicfeatures)
7232 ("r-genomicranges" ,r-genomicranges)
7233 ("r-ggplot2" ,r-ggplot2)
7234 ("r-ggpubr" ,r-ggpubr)
7235 ("r-graph" ,r-graph)
7237 ("r-iranges" ,r-iranges)
7238 ("r-magrittr" ,r-magrittr)
7240 ("r-rgraphviz" ,r-rgraphviz)
7241 ("r-rjson" ,r-rjson)
7242 ("r-s4vectors" ,r-s4vectors)
7243 ("r-scales" ,r-scales)
7244 ("r-shiny" ,r-shiny)
7245 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7246 (home-page "https://bioconductor.org/packages/BiocOncoTK")
7247 (synopsis "Bioconductor components for general cancer genomics")
7249 "The purpose of this package is to provide a central interface to various
7250 tools for genome-scale analysis of cancer studies.")
7251 (license license:artistic2.0)))
7253 (define-public r-biocor
7260 (uri (bioconductor-uri "BioCor" version))
7263 "1bjw02rwmz2d715sgpfp08njb15200ch7cmipsf9hd5835ppg1jl"))))
7264 (properties `((upstream-name . "BioCor")))
7265 (build-system r-build-system)
7267 `(("r-biocparallel" ,r-biocparallel)
7268 ("r-gseabase" ,r-gseabase)
7269 ("r-matrix" ,r-matrix)))
7270 (home-page "https://llrs.github.io/BioCor/")
7271 (synopsis "Functional similarities")
7273 "This package provides tools to calculate functional similarities based
7274 on the pathways described on KEGG and REACTOME or in gene sets. These
7275 similarities can be calculated for pathways or gene sets, genes, or clusters
7276 and combined with other similarities. They can be used to improve networks,
7277 gene selection, testing relationships, and so on.")
7278 (license license:expat)))
7280 (define-public r-biocpkgtools
7282 (name "r-biocpkgtools")
7287 (uri (bioconductor-uri "BiocPkgTools" version))
7290 "0gyhb3071pxmvaxla7cxy9k97s3z3ynl62jnqz9jnkd53c7jnd53"))))
7291 (properties `((upstream-name . "BiocPkgTools")))
7292 (build-system r-build-system)
7294 `(("r-biocmanager" ,r-biocmanager)
7295 ("r-biocviews" ,r-biocviews)
7296 ("r-dplyr" ,r-dplyr)
7299 ("r-graph" ,r-graph)
7300 ("r-htmltools" ,r-htmltools)
7301 ("r-htmlwidgets" ,r-htmlwidgets)
7303 ("r-igraph" ,r-igraph)
7304 ("r-jsonlite" ,r-jsonlite)
7305 ("r-magrittr" ,r-magrittr)
7307 ("r-readr" ,r-readr)
7309 ("r-rvest" ,r-rvest)
7310 ("r-stringr" ,r-stringr)
7311 ("r-tibble" ,r-tibble)
7312 ("r-tidyr" ,r-tidyr)
7313 ("r-xml2" ,r-xml2)))
7314 (home-page "https://github.com/seandavi/BiocPkgTools")
7315 (synopsis "Collection of tools for learning about Bioconductor packages")
7317 "Bioconductor has a rich ecosystem of metadata around packages, usage,
7318 and build status. This package is a simple collection of functions to access
7319 that metadata from R. The goal is to expose metadata for data mining and
7320 value-added functionality such as package searching, text mining, and
7321 analytics on packages.")
7322 (license license:expat)))
7324 (define-public r-biocset
7331 (uri (bioconductor-uri "BiocSet" version))
7334 "1xcksnvjflrdarn8xqmgf0n6wbsjkq9jazqwp35i52vqcq4ic1j9"))))
7335 (properties `((upstream-name . "BiocSet")))
7336 (build-system r-build-system)
7338 `(("r-annotationdbi" ,r-annotationdbi)
7339 ("r-dplyr" ,r-dplyr)
7340 ("r-keggrest" ,r-keggrest)
7342 ("r-rlang" ,r-rlang)
7343 ("r-rtracklayer" ,r-rtracklayer)
7344 ("r-tibble" ,r-tibble)))
7346 "https://bioconductor.org/packages/BiocSet")
7348 "Representing Different Biological Sets")
7350 "BiocSet displays different biological sets in a triple tibble format.
7351 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
7352 The user has the abilty to activate one of these three tibbles to perform
7353 common functions from the @code{dplyr} package. Mapping functionality and
7354 accessing web references for elements/sets are also available in BiocSet.")
7355 (license license:artistic2.0)))
7357 (define-public r-biocworkflowtools
7359 (name "r-biocworkflowtools")
7364 (uri (bioconductor-uri "BiocWorkflowTools" version))
7367 "1v4bhnpdkmllm7aghms9b7369hkrgz7mn69wbrqg1x42pgkf30ad"))))
7369 `((upstream-name . "BiocWorkflowTools")))
7370 (build-system r-build-system)
7372 `(("r-biocstyle" ,r-biocstyle)
7373 ("r-bookdown" ,r-bookdown)
7374 ("r-git2r" ,r-git2r)
7376 ("r-knitr" ,r-knitr)
7377 ("r-rmarkdown" ,r-rmarkdown)
7378 ("r-rstudioapi" ,r-rstudioapi)
7379 ("r-stringr" ,r-stringr)
7380 ("r-usethis" ,r-usethis)))
7381 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
7382 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
7384 "This package provides functions to ease the transition between
7385 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
7386 (license license:expat)))
7388 (define-public r-biodist
7395 (uri (bioconductor-uri "bioDist" version))
7398 "0iabw07px3ybdgbbab0vv350051cm4aq8w47rz9dnmzx4kil9h5q"))))
7399 (properties `((upstream-name . "bioDist")))
7400 (build-system r-build-system)
7402 `(("r-biobase" ,r-biobase)
7403 ("r-kernsmooth" ,r-kernsmooth)))
7404 (home-page "https://bioconductor.org/packages/bioDist/")
7405 (synopsis "Different distance measures")
7407 "This package provides a collection of software tools for calculating
7408 distance measures.")
7409 (license license:artistic2.0)))