1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2016, 2017, 2018, 2019 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>
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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 "0cgy9phwdk4x9lr11xh6zs7v8r5xq959fmsmzwrpnd50dr7hzkvd"))))
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-ggplot2" ,r-ggplot2)
1075 ("r-gostats" ,r-gostats)
1076 ("r-gplots" ,r-gplots)
1077 ("r-hwriter" ,r-hwriter)
1078 ("r-lattice" ,r-lattice)
1079 ("r-limma" ,r-limma)
1080 ("r-oligoclasses" ,r-oligoclasses)
1081 ("r-reportingtools" ,r-reportingtools)
1082 ("r-rsqlite" ,r-rsqlite)
1083 ("r-s4vectors" ,r-s4vectors)
1084 ("r-xtable" ,r-xtable)))
1085 (home-page "https://bioconductor.org/packages/affycoretools/")
1086 (synopsis "Functions for analyses with Affymetrix GeneChips")
1088 "This package provides various wrapper functions that have been written
1089 to streamline the more common analyses that a Biostatistician might see.")
1090 (license license:artistic2.0)))
1092 (define-public r-affxparser
1094 (name "r-affxparser")
1099 (uri (bioconductor-uri "affxparser" version))
1102 "03h4lxr48p84f6i7zb2rm10ma3k4d1nmvdw5yhxcmzqbmd12lk40"))))
1103 (properties `((upstream-name . "affxparser")))
1104 (build-system r-build-system)
1105 (home-page "https://github.com/HenrikBengtsson/affxparser")
1106 (synopsis "Affymetrix File Parsing SDK")
1108 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1109 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1110 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1111 are supported. Currently, there are methods for reading @dfn{chip definition
1112 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1113 either in full or in part. For example, probe signals from a few probesets
1114 can be extracted very quickly from a set of CEL files into a convenient list
1116 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1118 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1120 (define-public r-annotate
1127 (uri (bioconductor-uri "annotate" version))
1130 "0rcmdy6hs6m4d6wxgi52c0bhdsbf2sm9f155qbcb05sn0nh8pxwy"))))
1131 (build-system r-build-system)
1133 `(("r-annotationdbi" ,r-annotationdbi)
1134 ("r-biobase" ,r-biobase)
1135 ("r-biocgenerics" ,r-biocgenerics)
1137 ("r-rcurl" ,r-rcurl)
1139 ("r-xtable" ,r-xtable)))
1141 "https://bioconductor.org/packages/annotate")
1142 (synopsis "Annotation for microarrays")
1143 (description "This package provides R environments for the annotation of
1145 (license license:artistic2.0)))
1147 (define-public r-hpar
1154 (uri (bioconductor-uri "hpar" version))
1157 "1yhay1ryrgj9cqa1x136cw40ca93afyvg0sarm30jsbj8nc1rm5m"))))
1158 (build-system r-build-system)
1159 (home-page "https://bioconductor.org/packages/hpar/")
1160 (synopsis "Human Protein Atlas in R")
1161 (description "This package provides a simple interface to and data from
1162 the Human Protein Atlas project.")
1163 (license license:artistic2.0)))
1165 (define-public r-regioner
1172 (uri (bioconductor-uri "regioneR" version))
1175 "0m073hrqp62zpd2blnqm5ka539hcilir05m8av14vdhzhjzp13ya"))))
1176 (properties `((upstream-name . "regioneR")))
1177 (build-system r-build-system)
1179 `(("r-biostrings" ,r-biostrings)
1180 ("r-bsgenome" ,r-bsgenome)
1181 ("r-genomeinfodb" ,r-genomeinfodb)
1182 ("r-genomicranges" ,r-genomicranges)
1183 ("r-iranges" ,r-iranges)
1184 ("r-memoise" ,r-memoise)
1185 ("r-rtracklayer" ,r-rtracklayer)
1186 ("r-s4vectors" ,r-s4vectors)))
1187 (home-page "https://bioconductor.org/packages/regioneR/")
1188 (synopsis "Association analysis of genomic regions")
1189 (description "This package offers a statistical framework based on
1190 customizable permutation tests to assess the association between genomic
1191 region sets and other genomic features.")
1192 (license license:artistic2.0)))
1194 (define-public r-reportingtools
1196 (name "r-reportingtools")
1201 (uri (bioconductor-uri "ReportingTools" version))
1204 "0wmi2219wydyzc07rz3azsrksa7wiacfh9pr5x2fsmj9f0w3n15w"))))
1206 `((upstream-name . "ReportingTools")))
1207 (build-system r-build-system)
1209 `(("r-annotate" ,r-annotate)
1210 ("r-annotationdbi" ,r-annotationdbi)
1211 ("r-biobase" ,r-biobase)
1212 ("r-biocgenerics" ,r-biocgenerics)
1213 ("r-category" ,r-category)
1214 ("r-deseq2" ,r-deseq2)
1215 ("r-edger" ,r-edger)
1216 ("r-ggbio" ,r-ggbio)
1217 ("r-ggplot2" ,r-ggplot2)
1218 ("r-gostats" ,r-gostats)
1219 ("r-gseabase" ,r-gseabase)
1220 ("r-hwriter" ,r-hwriter)
1221 ("r-iranges" ,r-iranges)
1222 ("r-knitr" ,r-knitr)
1223 ("r-lattice" ,r-lattice)
1224 ("r-limma" ,r-limma)
1225 ("r-pfam-db" ,r-pfam-db)
1226 ("r-r-utils" ,r-r-utils)
1228 (home-page "https://bioconductor.org/packages/ReportingTools/")
1229 (synopsis "Tools for making reports in various formats")
1231 "The ReportingTools package enables users to easily display reports of
1232 analysis results generated from sources such as microarray and sequencing
1233 data. The package allows users to create HTML pages that may be viewed on a
1234 web browser, or in other formats. Users can generate tables with sortable and
1235 filterable columns, make and display plots, and link table entries to other
1236 data sources such as NCBI or larger plots within the HTML page. Using the
1237 package, users can also produce a table of contents page to link various
1238 reports together for a particular project that can be viewed in a web
1240 (license license:artistic2.0)))
1242 (define-public r-geneplotter
1244 (name "r-geneplotter")
1249 (uri (bioconductor-uri "geneplotter" version))
1252 "1k6780fn1kkghpm1prhhsyw621441a3bmnqfl9ns0zbc1zdq39nx"))))
1253 (build-system r-build-system)
1255 `(("r-annotate" ,r-annotate)
1256 ("r-annotationdbi" ,r-annotationdbi)
1257 ("r-biobase" ,r-biobase)
1258 ("r-biocgenerics" ,r-biocgenerics)
1259 ("r-lattice" ,r-lattice)
1260 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1261 (home-page "https://bioconductor.org/packages/geneplotter")
1262 (synopsis "Graphics functions for genomic data")
1264 "This package provides functions for plotting genomic data.")
1265 (license license:artistic2.0)))
1267 (define-public r-oligoclasses
1269 (name "r-oligoclasses")
1274 (uri (bioconductor-uri "oligoClasses" version))
1277 "02m1m3dkiyywalphw3i5n6y3bs8zp24xh59v9cz6jgjpah811skf"))))
1278 (properties `((upstream-name . "oligoClasses")))
1279 (build-system r-build-system)
1281 `(("r-affyio" ,r-affyio)
1282 ("r-biobase" ,r-biobase)
1283 ("r-biocgenerics" ,r-biocgenerics)
1284 ("r-biocmanager" ,r-biocmanager)
1285 ("r-biostrings" ,r-biostrings)
1288 ("r-foreach" ,r-foreach)
1289 ("r-genomicranges" ,r-genomicranges)
1290 ("r-iranges" ,r-iranges)
1291 ("r-rsqlite" ,r-rsqlite)
1292 ("r-s4vectors" ,r-s4vectors)
1293 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1294 (home-page "https://bioconductor.org/packages/oligoClasses/")
1295 (synopsis "Classes for high-throughput arrays")
1297 "This package contains class definitions, validity checks, and
1298 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1300 (license license:gpl2+)))
1302 (define-public r-oligo
1309 (uri (bioconductor-uri "oligo" version))
1312 "01icfyy82f9k0m7ngrppz1ckq3wpq7zp6kgf8ppc55j6582c5jh3"))))
1313 (properties `((upstream-name . "oligo")))
1314 (build-system r-build-system)
1315 (inputs `(("zlib" ,zlib)))
1317 `(("r-affxparser" ,r-affxparser)
1318 ("r-affyio" ,r-affyio)
1319 ("r-biobase" ,r-biobase)
1320 ("r-biocgenerics" ,r-biocgenerics)
1321 ("r-biostrings" ,r-biostrings)
1324 ("r-oligoclasses" ,r-oligoclasses)
1325 ("r-preprocesscore" ,r-preprocesscore)
1326 ("r-rsqlite" ,r-rsqlite)
1327 ("r-zlibbioc" ,r-zlibbioc)))
1328 (home-page "https://bioconductor.org/packages/oligo/")
1329 (synopsis "Preprocessing tools for oligonucleotide arrays")
1331 "This package provides a package to analyze oligonucleotide
1332 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1333 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1334 (license license:lgpl2.0+)))
1336 (define-public r-qvalue
1343 (uri (bioconductor-uri "qvalue" version))
1346 "0njnidyncm3g3712mnp77cs4kghn596ss1pz6fhp1cr0wxcayp6j"))))
1347 (build-system r-build-system)
1349 `(("r-ggplot2" ,r-ggplot2)
1350 ("r-reshape2" ,r-reshape2)))
1351 (home-page "http://github.com/jdstorey/qvalue")
1352 (synopsis "Q-value estimation for false discovery rate control")
1354 "This package takes a list of p-values resulting from the simultaneous
1355 testing of many hypotheses and estimates their q-values and local @dfn{false
1356 discovery rate} (FDR) values. The q-value of a test measures the proportion
1357 of false positives incurred when that particular test is called significant.
1358 The local FDR measures the posterior probability the null hypothesis is true
1359 given the test's p-value. Various plots are automatically generated, allowing
1360 one to make sensible significance cut-offs. The software can be applied to
1361 problems in genomics, brain imaging, astrophysics, and data mining.")
1362 ;; Any version of the LGPL.
1363 (license license:lgpl3+)))
1365 (define-public r-diffbind
1372 (uri (bioconductor-uri "DiffBind" version))
1375 "1729wyi2l4480yrkp5wg3ryirrmlk0j3njqs1qyckq3c8bjk12h2"))))
1376 (properties `((upstream-name . "DiffBind")))
1377 (build-system r-build-system)
1381 `(("r-amap" ,r-amap)
1382 ("r-biocparallel" ,r-biocparallel)
1383 ("r-deseq2" ,r-deseq2)
1384 ("r-dplyr" ,r-dplyr)
1385 ("r-edger" ,r-edger)
1386 ("r-genomicalignments" ,r-genomicalignments)
1387 ("r-genomicranges" ,r-genomicranges)
1388 ("r-ggplot2" ,r-ggplot2)
1389 ("r-ggrepel" ,r-ggrepel)
1390 ("r-gplots" ,r-gplots)
1391 ("r-iranges" ,r-iranges)
1392 ("r-lattice" ,r-lattice)
1393 ("r-limma" ,r-limma)
1394 ("r-locfit" ,r-locfit)
1395 ("r-rcolorbrewer" , r-rcolorbrewer)
1397 ("r-rhtslib" ,r-rhtslib)
1398 ("r-rsamtools" ,r-rsamtools)
1399 ("r-s4vectors" ,r-s4vectors)
1400 ("r-summarizedexperiment" ,r-summarizedexperiment)
1401 ("r-systempiper" ,r-systempiper)))
1402 (home-page "http://bioconductor.org/packages/DiffBind")
1403 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1405 "This package computes differentially bound sites from multiple
1406 ChIP-seq experiments using affinity (quantitative) data. Also enables
1407 occupancy (overlap) analysis and plotting functions.")
1408 (license license:artistic2.0)))
1410 (define-public r-ripseeker
1412 (name "r-ripseeker")
1417 (uri (bioconductor-uri "RIPSeeker" version))
1420 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
1421 (properties `((upstream-name . "RIPSeeker")))
1422 (build-system r-build-system)
1424 `(("r-s4vectors" ,r-s4vectors)
1425 ("r-iranges" ,r-iranges)
1426 ("r-genomicranges" ,r-genomicranges)
1427 ("r-summarizedexperiment" ,r-summarizedexperiment)
1428 ("r-rsamtools" ,r-rsamtools)
1429 ("r-genomicalignments" ,r-genomicalignments)
1430 ("r-rtracklayer" ,r-rtracklayer)))
1431 (home-page "http://bioconductor.org/packages/RIPSeeker")
1433 "Identifying protein-associated transcripts from RIP-seq experiments")
1435 "This package infers and discriminates RIP peaks from RIP-seq alignments
1436 using two-state HMM with negative binomial emission probability. While
1437 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1438 a suite of bioinformatics tools integrated within this self-contained software
1439 package comprehensively addressing issues ranging from post-alignments
1440 processing to visualization and annotation.")
1441 (license license:gpl2)))
1443 (define-public r-multtest
1450 (uri (bioconductor-uri "multtest" version))
1453 "0qna9lx76ldsfy8qf5xmhl4ymqfkj29m1gdqhph06s470c8mwari"))))
1454 (build-system r-build-system)
1456 `(("r-survival" ,r-survival)
1457 ("r-biocgenerics" ,r-biocgenerics)
1458 ("r-biobase" ,r-biobase)
1459 ("r-mass" ,r-mass)))
1460 (home-page "http://bioconductor.org/packages/multtest")
1461 (synopsis "Resampling-based multiple hypothesis testing")
1463 "This package can do non-parametric bootstrap and permutation
1464 resampling-based multiple testing procedures (including empirical Bayes
1465 methods) for controlling the family-wise error rate (FWER), generalized
1466 family-wise error rate (gFWER), tail probability of the proportion of
1467 false positives (TPPFP), and false discovery rate (FDR). Several choices
1468 of bootstrap-based null distribution are implemented (centered, centered
1469 and scaled, quantile-transformed). Single-step and step-wise methods are
1470 available. Tests based on a variety of T- and F-statistics (including
1471 T-statistics based on regression parameters from linear and survival models
1472 as well as those based on correlation parameters) are included. When probing
1473 hypotheses with T-statistics, users may also select a potentially faster null
1474 distribution which is multivariate normal with mean zero and variance
1475 covariance matrix derived from the vector influence function. Results are
1476 reported in terms of adjusted P-values, confidence regions and test statistic
1477 cutoffs. The procedures are directly applicable to identifying differentially
1478 expressed genes in DNA microarray experiments.")
1479 (license license:lgpl3)))
1481 (define-public r-graph
1487 (uri (bioconductor-uri "graph" version))
1490 "1ivf59k7k552m7zd8g3wwazd71dq3xmgmhcq435738i02h0fqnyc"))))
1491 (build-system r-build-system)
1493 `(("r-biocgenerics" ,r-biocgenerics)))
1494 (home-page "https://bioconductor.org/packages/graph")
1495 (synopsis "Handle graph data structures in R")
1497 "This package implements some simple graph handling capabilities for R.")
1498 (license license:artistic2.0)))
1500 (define-public r-codedepends
1502 (name "r-codedepends")
1507 (uri (cran-uri "CodeDepends" version))
1510 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1511 (properties `((upstream-name . "CodeDepends")))
1512 (build-system r-build-system)
1514 `(("r-codetools" ,r-codetools)
1515 ("r-graph" ,r-graph)
1517 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1518 (synopsis "Analysis of R code for reproducible research and code comprehension")
1520 "This package provides tools for analyzing R expressions or blocks of
1521 code and determining the dependencies between them. It focuses on R scripts,
1522 but can be used on the bodies of functions. There are many facilities
1523 including the ability to summarize or get a high-level view of code,
1524 determining dependencies between variables, code improvement suggestions.")
1525 ;; Any version of the GPL
1526 (license (list license:gpl2+ license:gpl3+))))
1528 (define-public r-chippeakanno
1530 (name "r-chippeakanno")
1535 (uri (bioconductor-uri "ChIPpeakAnno" version))
1538 "0hp3s3shnrb55cxvx9wrdl67wqw9f55gdgx7262s4mahpxjswfsa"))))
1539 (properties `((upstream-name . "ChIPpeakAnno")))
1540 (build-system r-build-system)
1542 `(("r-annotationdbi" ,r-annotationdbi)
1543 ("r-biobase" ,r-biobase)
1544 ("r-biocgenerics" ,r-biocgenerics)
1545 ("r-biocmanager" ,r-biocmanager)
1546 ("r-biomart" ,r-biomart)
1547 ("r-biostrings" ,r-biostrings)
1548 ("r-bsgenome" ,r-bsgenome)
1550 ("r-delayedarray" ,r-delayedarray)
1551 ("r-ensembldb" ,r-ensembldb)
1552 ("r-genomeinfodb" ,r-genomeinfodb)
1553 ("r-genomicalignments" ,r-genomicalignments)
1554 ("r-genomicfeatures" ,r-genomicfeatures)
1555 ("r-genomicranges" ,r-genomicranges)
1556 ("r-go-db" ,r-go-db)
1557 ("r-graph" ,r-graph)
1559 ("r-iranges" ,r-iranges)
1560 ("r-limma" ,r-limma)
1561 ("r-matrixstats" ,r-matrixstats)
1562 ("r-multtest" ,r-multtest)
1564 ("r-regioner" ,r-regioner)
1565 ("r-rsamtools" ,r-rsamtools)
1566 ("r-rtracklayer" ,r-rtracklayer)
1567 ("r-s4vectors" ,r-s4vectors)
1568 ("r-seqinr" ,r-seqinr)
1569 ("r-summarizedexperiment" ,r-summarizedexperiment)
1570 ("r-venndiagram" ,r-venndiagram)))
1571 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1572 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1574 "The package includes functions to retrieve the sequences around the peak,
1575 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1576 custom features such as most conserved elements and other transcription factor
1577 binding sites supplied by users. Starting 2.0.5, new functions have been added
1578 for finding the peaks with bi-directional promoters with summary statistics
1579 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1580 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1581 enrichedGO (addGeneIDs).")
1582 (license license:gpl2+)))
1584 (define-public r-marray
1590 (uri (bioconductor-uri "marray" version))
1592 (base32 "1mbs9rk279hnm9yz34za3xz3hb88ll1d0abw4m2pgjgbh4kkhdrl"))))
1593 (build-system r-build-system)
1595 `(("r-limma" ,r-limma)))
1596 (home-page "http://bioconductor.org/packages/marray")
1597 (synopsis "Exploratory analysis for two-color spotted microarray data")
1598 (description "This package contains class definitions for two-color spotted
1599 microarray data. It also includes functions for data input, diagnostic plots,
1600 normalization and quality checking.")
1601 (license license:lgpl2.0+)))
1603 (define-public r-cghbase
1609 (uri (bioconductor-uri "CGHbase" version))
1611 (base32 "0136pk6pfwpiiy9vca4pgg4wh74jfb5ssglpdszzhamljpvg765x"))))
1612 (properties `((upstream-name . "CGHbase")))
1613 (build-system r-build-system)
1615 `(("r-biobase" ,r-biobase)
1616 ("r-marray" ,r-marray)))
1617 (home-page "http://bioconductor.org/packages/CGHbase")
1618 (synopsis "Base functions and classes for arrayCGH data analysis")
1619 (description "This package contains functions and classes that are needed by
1620 the @code{arrayCGH} packages.")
1621 (license license:gpl2+)))
1623 (define-public r-cghcall
1629 (uri (bioconductor-uri "CGHcall" version))
1631 (base32 "1x8pz7zhw2nabik1vgdhlivndqvil3s7vnl5070k493v6gza0p3s"))))
1632 (properties `((upstream-name . "CGHcall")))
1633 (build-system r-build-system)
1635 `(("r-biobase" ,r-biobase)
1636 ("r-cghbase" ,r-cghbase)
1637 ("r-impute" ,r-impute)
1638 ("r-dnacopy" ,r-dnacopy)
1639 ("r-snowfall" ,r-snowfall)))
1640 (home-page "http://bioconductor.org/packages/CGHcall")
1641 (synopsis "Base functions and classes for arrayCGH data analysis")
1642 (description "This package contains functions and classes that are needed by
1643 @code{arrayCGH} packages.")
1644 (license license:gpl2+)))
1646 (define-public r-qdnaseq
1652 (uri (bioconductor-uri "QDNAseq" version))
1654 (base32 "0xcqdpv9a47zpxx0q9sif5y4s1yzx3pig0kywy961kh5xgl5bcrq"))))
1655 (properties `((upstream-name . "QDNAseq")))
1656 (build-system r-build-system)
1658 `(("r-biobase" ,r-biobase)
1659 ("r-cghbase" ,r-cghbase)
1660 ("r-cghcall" ,r-cghcall)
1661 ("r-dnacopy" ,r-dnacopy)
1662 ("r-future" ,r-future)
1663 ("r-future-apply" ,r-future-apply)
1664 ("r-genomicranges" ,r-genomicranges)
1665 ("r-iranges" ,r-iranges)
1666 ("r-matrixstats" ,r-matrixstats)
1667 ("r-r-utils" ,r-r-utils)
1668 ("r-rsamtools" ,r-rsamtools)))
1669 (home-page "http://bioconductor.org/packages/QDNAseq")
1670 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1671 (description "The genome is divided into non-overlapping fixed-sized bins,
1672 number of sequence reads in each counted, adjusted with a simultaneous
1673 two-dimensional loess correction for sequence mappability and GC content, and
1674 filtered to remove spurious regions in the genome. Downstream steps of
1675 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1677 (license license:gpl2+)))
1679 (define-public r-bayseq
1686 (uri (bioconductor-uri "baySeq" version))
1689 "040s1d3756spyzblkyx2vcy7bn3vf87mhsp3is35yxkj55n3myjk"))))
1690 (properties `((upstream-name . "baySeq")))
1691 (build-system r-build-system)
1693 `(("r-abind" ,r-abind)
1694 ("r-edger" ,r-edger)
1695 ("r-genomicranges" ,r-genomicranges)))
1696 (home-page "https://bioconductor.org/packages/baySeq/")
1697 (synopsis "Bayesian analysis of differential expression patterns in count data")
1699 "This package identifies differential expression in high-throughput count
1700 data, such as that derived from next-generation sequencing machines,
1701 calculating estimated posterior likelihoods of differential expression (or
1702 more complex hypotheses) via empirical Bayesian methods.")
1703 (license license:gpl3)))
1705 (define-public r-chipcomp
1712 (uri (bioconductor-uri "ChIPComp" version))
1715 "0wk0vvg6dk9wk60lzbadrnqar75dppvyr4hiwrhv9rhhah2mg2mg"))))
1716 (properties `((upstream-name . "ChIPComp")))
1717 (build-system r-build-system)
1719 `(("r-biocgenerics" ,r-biocgenerics)
1720 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1721 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1722 ("r-genomeinfodb" ,r-genomeinfodb)
1723 ("r-genomicranges" ,r-genomicranges)
1724 ("r-iranges" ,r-iranges)
1725 ("r-limma" ,r-limma)
1726 ("r-rsamtools" ,r-rsamtools)
1727 ("r-rtracklayer" ,r-rtracklayer)
1728 ("r-s4vectors" ,r-s4vectors)))
1729 (home-page "https://bioconductor.org/packages/ChIPComp")
1730 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1732 "ChIPComp implements a statistical method for quantitative comparison of
1733 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1734 sites across multiple conditions considering matching control in ChIP-seq
1736 ;; Any version of the GPL.
1737 (license license:gpl3+)))
1739 (define-public r-riboprofiling
1741 (name "r-riboprofiling")
1746 (uri (bioconductor-uri "RiboProfiling" version))
1749 "0nfzyiq7cd6fs5agzl1zyfg8s631wi7kjngiyvd3vxlhi8wsjicx"))))
1750 (properties `((upstream-name . "RiboProfiling")))
1751 (build-system r-build-system)
1753 `(("r-biocgenerics" ,r-biocgenerics)
1754 ("r-biostrings" ,r-biostrings)
1755 ("r-data-table" ,r-data-table)
1756 ("r-genomeinfodb" ,r-genomeinfodb)
1757 ("r-genomicalignments" ,r-genomicalignments)
1758 ("r-genomicfeatures" ,r-genomicfeatures)
1759 ("r-genomicranges" ,r-genomicranges)
1760 ("r-ggbio" ,r-ggbio)
1761 ("r-ggplot2" ,r-ggplot2)
1762 ("r-iranges" ,r-iranges)
1764 ("r-reshape2" ,r-reshape2)
1765 ("r-rsamtools" ,r-rsamtools)
1766 ("r-rtracklayer" ,r-rtracklayer)
1767 ("r-s4vectors" ,r-s4vectors)
1768 ("r-sqldf" ,r-sqldf)))
1769 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1770 (synopsis "Ribosome profiling data analysis")
1771 (description "Starting with a BAM file, this package provides the
1772 necessary functions for quality assessment, read start position recalibration,
1773 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1774 of count data: pairs, log fold-change, codon frequency and coverage
1775 assessment, principal component analysis on codon coverage.")
1776 (license license:gpl3)))
1778 (define-public r-riboseqr
1785 (uri (bioconductor-uri "riboSeqR" version))
1788 "1jr7h64hyhyf9gf15lah6iqwyljfc8mraf9kya4lql6lcjjkjiqm"))))
1789 (properties `((upstream-name . "riboSeqR")))
1790 (build-system r-build-system)
1792 `(("r-abind" ,r-abind)
1793 ("r-bayseq" ,r-bayseq)
1794 ("r-genomeinfodb" ,r-genomeinfodb)
1795 ("r-genomicranges" ,r-genomicranges)
1796 ("r-iranges" ,r-iranges)
1797 ("r-rsamtools" ,r-rsamtools)
1798 ("r-seqlogo" ,r-seqlogo)))
1799 (home-page "https://bioconductor.org/packages/riboSeqR/")
1800 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1802 "This package provides plotting functions, frameshift detection and
1803 parsing of genetic sequencing data from ribosome profiling experiments.")
1804 (license license:gpl3)))
1806 (define-public r-interactionset
1808 (name "r-interactionset")
1813 (uri (bioconductor-uri "InteractionSet" version))
1816 "0n2l95h56x5g68p10cap8p4x3a6vaph2hjlk09vmi3j48lrzb2kh"))))
1818 `((upstream-name . "InteractionSet")))
1819 (build-system r-build-system)
1821 `(("r-biocgenerics" ,r-biocgenerics)
1822 ("r-genomeinfodb" ,r-genomeinfodb)
1823 ("r-genomicranges" ,r-genomicranges)
1824 ("r-iranges" ,r-iranges)
1825 ("r-matrix" ,r-matrix)
1827 ("r-s4vectors" ,r-s4vectors)
1828 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1829 (home-page "https://bioconductor.org/packages/InteractionSet")
1830 (synopsis "Base classes for storing genomic interaction data")
1832 "This package provides the @code{GInteractions},
1833 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1834 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1836 (license license:gpl3)))
1838 (define-public r-genomicinteractions
1840 (name "r-genomicinteractions")
1845 (uri (bioconductor-uri "GenomicInteractions" version))
1848 "10kwb70c9aq0bfqpq48h186lsbwgrg18m14r9z8x6n8l7cds5azc"))))
1850 `((upstream-name . "GenomicInteractions")))
1851 (build-system r-build-system)
1853 `(("r-biobase" ,r-biobase)
1854 ("r-biocgenerics" ,r-biocgenerics)
1855 ("r-data-table" ,r-data-table)
1856 ("r-dplyr" ,r-dplyr)
1857 ("r-genomeinfodb" ,r-genomeinfodb)
1858 ("r-genomicranges" ,r-genomicranges)
1859 ("r-ggplot2" ,r-ggplot2)
1860 ("r-gridextra" ,r-gridextra)
1862 ("r-igraph" ,r-igraph)
1863 ("r-interactionset" ,r-interactionset)
1864 ("r-iranges" ,r-iranges)
1865 ("r-rsamtools" ,r-rsamtools)
1866 ("r-rtracklayer" ,r-rtracklayer)
1867 ("r-s4vectors" ,r-s4vectors)
1868 ("r-stringr" ,r-stringr)))
1869 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1870 (synopsis "R package for handling genomic interaction data")
1872 "This R package provides tools for handling genomic interaction data,
1873 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1874 information and producing various plots and statistics.")
1875 (license license:gpl3)))
1877 (define-public r-ctc
1884 (uri (bioconductor-uri "ctc" version))
1887 "0wh27izkyr1j26nznisw654mb5c94xpwjjkx7r6bhwg9ihxxcl6d"))))
1888 (build-system r-build-system)
1889 (propagated-inputs `(("r-amap" ,r-amap)))
1890 (home-page "https://bioconductor.org/packages/ctc/")
1891 (synopsis "Cluster and tree conversion")
1893 "This package provides tools for exporting and importing classification
1894 trees and clusters to other programs.")
1895 (license license:gpl2)))
1897 (define-public r-goseq
1904 (uri (bioconductor-uri "goseq" version))
1907 "11ypa41qv1nx3cncxlwlbhdxqlwq95rb9byv2z3crrf9nfp24byv"))))
1908 (build-system r-build-system)
1910 `(("r-annotationdbi" ,r-annotationdbi)
1911 ("r-biasedurn" ,r-biasedurn)
1912 ("r-biocgenerics" ,r-biocgenerics)
1913 ("r-genelendatabase" ,r-genelendatabase)
1914 ("r-go-db" ,r-go-db)
1915 ("r-mgcv" ,r-mgcv)))
1916 (home-page "https://bioconductor.org/packages/goseq/")
1917 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1919 "This package provides tools to detect Gene Ontology and/or other user
1920 defined categories which are over/under represented in RNA-seq data.")
1921 (license license:lgpl2.0+)))
1923 (define-public r-glimma
1930 (uri (bioconductor-uri "Glimma" version))
1933 "1rjrqgl96iz4b3xqpc174wgz7bqmc8gbm9ljag0y27kz29fwng8r"))))
1934 (properties `((upstream-name . "Glimma")))
1935 (build-system r-build-system)
1937 `(("r-edger" ,r-edger)
1938 ("r-jsonlite" ,r-jsonlite)
1939 ("r-s4vectors" ,r-s4vectors)))
1940 (home-page "https://github.com/Shians/Glimma")
1941 (synopsis "Interactive HTML graphics")
1943 "This package generates interactive visualisations for analysis of
1944 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1945 HTML page. The interactions are built on top of the popular static
1946 representations of analysis results in order to provide additional
1948 (license license:lgpl3)))
1950 (define-public r-rots
1957 (uri (bioconductor-uri "ROTS" version))
1960 "08mwlb0lpprys2b7vif8aj5bnprmn09mm79zz158gbhrv9j9d1qm"))))
1961 (properties `((upstream-name . "ROTS")))
1962 (build-system r-build-system)
1964 `(("r-biobase" ,r-biobase)
1965 ("r-rcpp" ,r-rcpp)))
1966 (home-page "https://bioconductor.org/packages/ROTS/")
1967 (synopsis "Reproducibility-Optimized Test Statistic")
1969 "This package provides tools for calculating the
1970 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1972 (license license:gpl2+)))
1974 (define-public r-plgem
1981 (uri (bioconductor-uri "plgem" version))
1984 "0fkyvcw2qxp4g527s9rzia45yapi0r6gbij7svisil8rbgfdp45v"))))
1985 (build-system r-build-system)
1987 `(("r-biobase" ,r-biobase)
1988 ("r-mass" ,r-mass)))
1989 (home-page "http://www.genopolis.it")
1990 (synopsis "Detect differential expression in microarray and proteomics datasets")
1992 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1993 model the variance-versus-mean dependence that exists in a variety of
1994 genome-wide datasets, including microarray and proteomics data. The use of
1995 PLGEM has been shown to improve the detection of differentially expressed
1996 genes or proteins in these datasets.")
1997 (license license:gpl2)))
1999 (define-public r-inspect
2006 (uri (bioconductor-uri "INSPEcT" version))
2009 "043066zygf2y2jp6dvfwl56hkzcdvkmymhjx3gh4mhi48l71zqv9"))))
2010 (properties `((upstream-name . "INSPEcT")))
2011 (build-system r-build-system)
2013 `(("r-biobase" ,r-biobase)
2014 ("r-biocgenerics" ,r-biocgenerics)
2015 ("r-biocparallel" ,r-biocparallel)
2016 ("r-deseq2" ,r-deseq2)
2017 ("r-desolve" ,r-desolve)
2018 ("r-genomeinfodb" ,r-genomeinfodb)
2019 ("r-genomicalignments" ,r-genomicalignments)
2020 ("r-genomicfeatures" ,r-genomicfeatures)
2021 ("r-genomicranges" ,r-genomicranges)
2022 ("r-iranges" ,r-iranges)
2023 ("r-kernsmooth" ,r-kernsmooth)
2024 ("r-plgem" ,r-plgem)
2026 ("r-rootsolve" ,r-rootsolve)
2027 ("r-rsamtools" ,r-rsamtools)
2028 ("r-s4vectors" ,r-s4vectors)
2029 ("r-shiny" ,r-shiny)
2030 ("r-summarizedexperiment" ,r-summarizedexperiment)
2031 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2032 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2033 (home-page "https://bioconductor.org/packages/INSPEcT")
2034 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2036 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2037 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2038 order to evaluate synthesis, processing and degradation rates and assess via
2039 modeling the rates that determines changes in mature mRNA levels.")
2040 (license license:gpl2)))
2042 (define-public r-dnabarcodes
2044 (name "r-dnabarcodes")
2049 (uri (bioconductor-uri "DNABarcodes" version))
2052 "0r2r9qc2qvf7rfl1h5ynvv3xd7n444zbc697s85qxqdpr4sxqmfd"))))
2053 (properties `((upstream-name . "DNABarcodes")))
2054 (build-system r-build-system)
2057 ("r-matrix" ,r-matrix)
2058 ("r-rcpp" ,r-rcpp)))
2059 (home-page "https://bioconductor.org/packages/DNABarcodes")
2060 (synopsis "Create and analyze DNA barcodes")
2062 "This package offers tools to create DNA barcode sets capable of
2063 correcting insertion, deletion, and substitution errors. Existing barcodes
2064 can be analyzed regarding their minimal, maximal and average distances between
2065 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2066 demultiplexed, i.e. assigned to their original reference barcode.")
2067 (license license:gpl2)))
2069 (define-public r-ruvseq
2076 (uri (bioconductor-uri "RUVSeq" version))
2079 "1ipbbzpngx988lsmwqv7vbmqm65m43xvsmipayfppkrr6jipzxrj"))))
2080 (properties `((upstream-name . "RUVSeq")))
2081 (build-system r-build-system)
2083 `(("r-biobase" ,r-biobase)
2084 ("r-edaseq" ,r-edaseq)
2085 ("r-edger" ,r-edger)
2086 ("r-mass" ,r-mass)))
2087 (home-page "https://github.com/drisso/RUVSeq")
2088 (synopsis "Remove unwanted variation from RNA-Seq data")
2090 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2091 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2093 (license license:artistic2.0)))
2095 (define-public r-biocneighbors
2097 (name "r-biocneighbors")
2102 (uri (bioconductor-uri "BiocNeighbors" version))
2105 "05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf"))))
2106 (properties `((upstream-name . "BiocNeighbors")))
2107 (build-system r-build-system)
2109 `(("r-biocparallel" ,r-biocparallel)
2110 ("r-matrix" ,r-matrix)
2112 ("r-rcppannoy" ,r-rcppannoy)
2113 ("r-rcpphnsw" ,r-rcpphnsw)
2114 ("r-s4vectors" ,r-s4vectors)))
2115 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2116 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2118 "This package implements exact and approximate methods for nearest
2119 neighbor detection, in a framework that allows them to be easily switched
2120 within Bioconductor packages or workflows. The exact algorithm is implemented
2121 using pre-clustering with the k-means algorithm. Functions are also provided
2122 to search for all neighbors within a given distance. Parallelization is
2123 achieved for all methods using the BiocParallel framework.")
2124 (license license:gpl3)))
2126 (define-public r-biocsingular
2128 (name "r-biocsingular")
2133 (uri (bioconductor-uri "BiocSingular" version))
2136 "0qd7r2k56ym7ivjgapxbk7fyj2d7396f1ad1hkgnicgyw1an5q1r"))))
2137 (properties `((upstream-name . "BiocSingular")))
2138 (build-system r-build-system)
2140 `(("r-beachmat" ,r-beachmat)
2141 ("r-biocgenerics" ,r-biocgenerics)
2142 ("r-biocparallel" ,r-biocparallel)
2143 ("r-delayedarray" ,r-delayedarray)
2144 ("r-irlba" ,r-irlba)
2145 ("r-matrix" ,r-matrix)
2148 ("r-s4vectors" ,r-s4vectors)))
2149 (home-page "https://github.com/LTLA/BiocSingular")
2150 (synopsis "Singular value decomposition for Bioconductor packages")
2152 "This package implements exact and approximate methods for singular value
2153 decomposition and principal components analysis, in a framework that allows
2154 them to be easily switched within Bioconductor packages or workflows. Where
2155 possible, parallelization is achieved using the BiocParallel framework.")
2156 (license license:gpl3)))
2158 (define-public r-destiny
2165 (uri (bioconductor-uri "destiny" version))
2168 "0vj9nk8g6i4vzm6cnzvbsqcvyk6fhmx0a0nxxrciarffyhqk81yz"))))
2169 (build-system r-build-system)
2171 `(("r-biobase" ,r-biobase)
2172 ("r-biocgenerics" ,r-biocgenerics)
2173 ("r-ggplot-multistats" ,r-ggplot-multistats)
2174 ("r-ggplot2" ,r-ggplot2)
2175 ("r-ggthemes" ,r-ggthemes)
2176 ("r-irlba" ,r-irlba)
2177 ("r-knn-covertree" ,r-knn-covertree)
2178 ("r-matrix" ,r-matrix)
2179 ("r-pcamethods" ,r-pcamethods)
2180 ("r-proxy" ,r-proxy)
2182 ("r-rcppeigen" ,r-rcppeigen)
2183 ("r-rcpphnsw" ,r-rcpphnsw)
2184 ("r-rspectra" ,r-rspectra)
2185 ("r-scales" ,r-scales)
2186 ("r-scatterplot3d" ,r-scatterplot3d)
2187 ("r-singlecellexperiment" ,r-singlecellexperiment)
2188 ("r-smoother" ,r-smoother)
2189 ("r-summarizedexperiment" ,r-summarizedexperiment)
2190 ("r-tidyr" ,r-tidyr)
2191 ("r-tidyselect" ,r-tidyselect)
2193 (home-page "https://bioconductor.org/packages/destiny/")
2194 (synopsis "Create and plot diffusion maps")
2195 (description "This package provides tools to create and plot diffusion
2197 ;; Any version of the GPL
2198 (license license:gpl3+)))
2200 (define-public r-savr
2207 (uri (bioconductor-uri "savR" version))
2210 "1lsnqjl6qxbj0wai05qb2wrxrhxq5iarv2livmvwiwv70iigqygf"))))
2211 (properties `((upstream-name . "savR")))
2212 (build-system r-build-system)
2214 `(("r-ggplot2" ,r-ggplot2)
2215 ("r-gridextra" ,r-gridextra)
2216 ("r-reshape2" ,r-reshape2)
2217 ("r-scales" ,r-scales)
2219 (home-page "https://github.com/bcalder/savR")
2220 (synopsis "Parse and analyze Illumina SAV files")
2222 "This package provides tools to parse Illumina Sequence Analysis
2223 Viewer (SAV) files, access data, and generate QC plots.")
2224 (license license:agpl3+)))
2226 (define-public r-chipexoqual
2228 (name "r-chipexoqual")
2233 (uri (bioconductor-uri "ChIPexoQual" version))
2236 "044n6kn16qczpdhp0w0z5x8xpr0rfs9s8q70rafgnvj7a2q1xdd0"))))
2237 (properties `((upstream-name . "ChIPexoQual")))
2238 (build-system r-build-system)
2240 `(("r-biocparallel" ,r-biocparallel)
2241 ("r-biovizbase" ,r-biovizbase)
2242 ("r-broom" ,r-broom)
2243 ("r-data-table" ,r-data-table)
2244 ("r-dplyr" ,r-dplyr)
2245 ("r-genomeinfodb" ,r-genomeinfodb)
2246 ("r-genomicalignments" ,r-genomicalignments)
2247 ("r-genomicranges" ,r-genomicranges)
2248 ("r-ggplot2" ,r-ggplot2)
2249 ("r-hexbin" ,r-hexbin)
2250 ("r-iranges" ,r-iranges)
2251 ("r-rcolorbrewer" ,r-rcolorbrewer)
2252 ("r-rmarkdown" ,r-rmarkdown)
2253 ("r-rsamtools" ,r-rsamtools)
2254 ("r-s4vectors" ,r-s4vectors)
2255 ("r-scales" ,r-scales)
2256 ("r-viridis" ,r-viridis)))
2257 (home-page "https://github.com/keleslab/ChIPexoQual")
2258 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2260 "This package provides a quality control pipeline for ChIP-exo/nexus
2262 (license license:gpl2+)))
2264 (define-public r-copynumber
2266 (name "r-copynumber")
2270 (uri (bioconductor-uri "copynumber" version))
2273 "0r6r1adj20x3ckm0dlipxlf1rzngr92xsxxpy81mqxf4jpmyr8gj"))))
2274 (build-system r-build-system)
2276 `(("r-s4vectors" ,r-s4vectors)
2277 ("r-iranges" ,r-iranges)
2278 ("r-genomicranges" ,r-genomicranges)
2279 ("r-biocgenerics" ,r-biocgenerics)))
2280 (home-page "https://bioconductor.org/packages/copynumber")
2281 (synopsis "Segmentation of single- and multi-track copy number data")
2283 "This package segments single- and multi-track copy number data by a
2284 penalized least squares regression method.")
2285 (license license:artistic2.0)))
2287 (define-public r-dnacopy
2294 (uri (bioconductor-uri "DNAcopy" version))
2297 "119z5lqhhw9ppg6s4dvbxk1kxf3wc55ibpm9b88c91s04yd7m9yw"))))
2298 (properties `((upstream-name . "DNAcopy")))
2299 (build-system r-build-system)
2300 (native-inputs `(("gfortran" ,gfortran)))
2301 (home-page "https://bioconductor.org/packages/DNAcopy")
2302 (synopsis "DNA copy number data analysis")
2304 "This package implements the @dfn{circular binary segmentation} (CBS)
2305 algorithm to segment DNA copy number data and identify genomic regions with
2306 abnormal copy number.")
2307 (license license:gpl2+)))
2309 ;; This is a CRAN package, but it uncharacteristically depends on a
2310 ;; Bioconductor package.
2311 (define-public r-htscluster
2313 (name "r-htscluster")
2318 (uri (cran-uri "HTSCluster" version))
2321 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2322 (properties `((upstream-name . "HTSCluster")))
2323 (build-system r-build-system)
2325 `(("r-capushe" ,r-capushe)
2326 ("r-edger" ,r-edger)
2327 ("r-plotrix" ,r-plotrix)))
2328 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2329 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2331 "This package provides a Poisson mixture model is implemented to cluster
2332 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2333 estimation is performed using either the EM or CEM algorithm, and the slope
2334 heuristics are used for model selection (i.e., to choose the number of
2336 (license license:gpl3+)))
2338 (define-public r-deds
2345 (uri (bioconductor-uri "DEDS" version))
2348 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
2349 (properties `((upstream-name . "DEDS")))
2350 (build-system r-build-system)
2351 (home-page "https://bioconductor.org/packages/DEDS/")
2352 (synopsis "Differential expression via distance summary for microarray data")
2354 "This library contains functions that calculate various statistics of
2355 differential expression for microarray data, including t statistics, fold
2356 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2357 also implements a new methodology called DEDS (Differential Expression via
2358 Distance Summary), which selects differentially expressed genes by integrating
2359 and summarizing a set of statistics using a weighted distance approach.")
2360 ;; Any version of the LGPL.
2361 (license license:lgpl3+)))
2363 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2365 (define-public r-nbpseq
2372 (uri (cran-uri "NBPSeq" version))
2375 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2376 (properties `((upstream-name . "NBPSeq")))
2377 (build-system r-build-system)
2379 `(("r-qvalue" ,r-qvalue)))
2380 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2381 (synopsis "Negative binomial models for RNA-Seq data")
2383 "This package provides negative binomial models for two-group comparisons
2384 and regression inferences from RNA-sequencing data.")
2385 (license license:gpl2)))
2387 (define-public r-ebseq
2394 (uri (bioconductor-uri "EBSeq" version))
2397 "0ay1vcccpc29r3vinlnwp9256345bfb346kg2y11kib4bnrabjb6"))))
2398 (properties `((upstream-name . "EBSeq")))
2399 (build-system r-build-system)
2401 `(("r-blockmodeling" ,r-blockmodeling)
2402 ("r-gplots" ,r-gplots)
2403 ("r-testthat" ,r-testthat)))
2404 (home-page "https://bioconductor.org/packages/EBSeq")
2405 (synopsis "Differential expression analysis of RNA-seq data")
2407 "This package provides tools for differential expression analysis at both
2408 gene and isoform level using RNA-seq data")
2409 (license license:artistic2.0)))
2411 (define-public r-lpsymphony
2413 (name "r-lpsymphony")
2418 (uri (bioconductor-uri "lpsymphony" version))
2421 "0j5j9kggh3l61vp6hpnqf45d5kzifksaj0sqhvs1zahmx2c1gfdv"))))
2422 (build-system r-build-system)
2424 `(("gfortran" ,gfortran)
2427 `(("pkg-config" ,pkg-config)))
2428 (home-page "http://r-forge.r-project.org/projects/rsymphony")
2429 (synopsis "Symphony integer linear programming solver in R")
2431 "This package was derived from Rsymphony. The package provides an R
2432 interface to SYMPHONY, a linear programming solver written in C++. The main
2433 difference between this package and Rsymphony is that it includes the solver
2434 source code, while Rsymphony expects to find header and library files on the
2435 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2436 to install interface to SYMPHONY.")
2437 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2438 ;; lpsimphony is released under the same terms.
2439 (license license:epl1.0)))
2441 (define-public r-ihw
2448 (uri (bioconductor-uri "IHW" version))
2451 "0rnw7r9pylpj3a5graavcpiqv2v67rv2a4dlcynkf4ihpxs4bg8x"))))
2452 (properties `((upstream-name . "IHW")))
2453 (build-system r-build-system)
2455 `(("r-biocgenerics" ,r-biocgenerics)
2456 ("r-fdrtool" ,r-fdrtool)
2457 ("r-lpsymphony" ,r-lpsymphony)
2458 ("r-slam" ,r-slam)))
2459 (home-page "https://bioconductor.org/packages/IHW")
2460 (synopsis "Independent hypothesis weighting")
2462 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2463 procedure that increases power compared to the method of Benjamini and
2464 Hochberg by assigning data-driven weights to each hypothesis. The input to
2465 IHW is a two-column table of p-values and covariates. The covariate can be
2466 any continuous-valued or categorical variable that is thought to be
2467 informative on the statistical properties of each hypothesis test, while it is
2468 independent of the p-value under the null hypothesis.")
2469 (license license:artistic2.0)))
2471 (define-public r-icobra
2478 (uri (bioconductor-uri "iCOBRA" version))
2481 "1l0yr2grpwmr3pc5h50p1j4nxyb1ddmc55l7rhxpp4igh4fq1avz"))))
2482 (properties `((upstream-name . "iCOBRA")))
2483 (build-system r-build-system)
2485 `(("r-dplyr" ,r-dplyr)
2487 ("r-ggplot2" ,r-ggplot2)
2488 ("r-limma" ,r-limma)
2489 ("r-reshape2" ,r-reshape2)
2491 ("r-scales" ,r-scales)
2492 ("r-shiny" ,r-shiny)
2493 ("r-shinybs" ,r-shinybs)
2494 ("r-shinydashboard" ,r-shinydashboard)
2495 ("r-upsetr" ,r-upsetr)))
2496 (home-page "https://bioconductor.org/packages/iCOBRA")
2497 (synopsis "Comparison and visualization of ranking and assignment methods")
2499 "This package provides functions for calculation and visualization of
2500 performance metrics for evaluation of ranking and binary
2501 classification (assignment) methods. It also contains a Shiny application for
2502 interactive exploration of results.")
2503 (license license:gpl2+)))
2505 (define-public r-mast
2512 (uri (bioconductor-uri "MAST" version))
2515 "1l78rrwkzyswpj6pgc9z8290fqrk4akba76invkkazpyh91r8gga"))))
2516 (properties `((upstream-name . "MAST")))
2517 (build-system r-build-system)
2519 `(("r-abind" ,r-abind)
2520 ("r-biobase" ,r-biobase)
2521 ("r-biocgenerics" ,r-biocgenerics)
2522 ("r-data-table" ,r-data-table)
2523 ("r-ggplot2" ,r-ggplot2)
2525 ("r-progress" ,r-progress)
2526 ("r-reshape2" ,r-reshape2)
2527 ("r-s4vectors" ,r-s4vectors)
2528 ("r-singlecellexperiment" ,r-singlecellexperiment)
2529 ("r-stringr" ,r-stringr)
2530 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2531 (home-page "https://github.com/RGLab/MAST/")
2532 (synopsis "Model-based analysis of single cell transcriptomics")
2534 "This package provides methods and models for handling zero-inflated
2535 single cell assay data.")
2536 (license license:gpl2+)))
2538 (define-public r-monocle
2545 (uri (bioconductor-uri "monocle" version))
2548 "18b9y592q48mbcp5w095qs1kaklq64v6dcnlpqhv3rwxvywygsz2"))))
2549 (build-system r-build-system)
2551 `(("r-biobase" ,r-biobase)
2552 ("r-biocgenerics" ,r-biocgenerics)
2553 ("r-biocviews" ,r-biocviews)
2554 ("r-cluster" ,r-cluster)
2555 ("r-combinat" ,r-combinat)
2556 ("r-ddrtree" ,r-ddrtree)
2557 ("r-densityclust" ,r-densityclust)
2558 ("r-dplyr" ,r-dplyr)
2559 ("r-fastica" ,r-fastica)
2560 ("r-ggplot2" ,r-ggplot2)
2561 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2562 ("r-igraph" ,r-igraph)
2563 ("r-irlba" ,r-irlba)
2564 ("r-limma" ,r-limma)
2566 ("r-matrix" ,r-matrix)
2567 ("r-matrixstats" ,r-matrixstats)
2568 ("r-pheatmap" ,r-pheatmap)
2570 ("r-proxy" ,r-proxy)
2571 ("r-qlcmatrix" ,r-qlcmatrix)
2574 ("r-reshape2" ,r-reshape2)
2575 ("r-rtsne" ,r-rtsne)
2577 ("r-stringr" ,r-stringr)
2578 ("r-tibble" ,r-tibble)
2580 ("r-viridis" ,r-viridis)))
2581 (home-page "https://bioconductor.org/packages/monocle")
2582 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2584 "Monocle performs differential expression and time-series analysis for
2585 single-cell expression experiments. It orders individual cells according to
2586 progress through a biological process, without knowing ahead of time which
2587 genes define progress through that process. Monocle also performs
2588 differential expression analysis, clustering, visualization, and other useful
2589 tasks on single cell expression data. It is designed to work with RNA-Seq and
2590 qPCR data, but could be used with other types as well.")
2591 (license license:artistic2.0)))
2593 (define-public r-monocle3
2601 (url "https://github.com/cole-trapnell-lab/monocle3.git")
2603 (file-name (git-file-name name version))
2606 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2607 (build-system r-build-system)
2609 `(("r-biobase" ,r-biobase)
2610 ("r-biocgenerics" ,r-biocgenerics)
2611 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2612 ("r-dplyr" ,r-dplyr)
2613 ("r-ggplot2" ,r-ggplot2)
2614 ("r-ggrepel" ,r-ggrepel)
2616 ("r-htmlwidgets" ,r-htmlwidgets)
2617 ("r-igraph" ,r-igraph)
2618 ("r-irlba" ,r-irlba)
2619 ("r-limma" ,r-limma)
2620 ("r-lmtest" ,r-lmtest)
2622 ("r-matrix" ,r-matrix)
2623 ("r-matrix-utils" ,r-matrix-utils)
2624 ("r-pbapply" ,r-pbapply)
2625 ("r-pbmcapply" ,r-pbmcapply)
2626 ("r-pheatmap" ,r-pheatmap)
2627 ("r-plotly" ,r-plotly)
2629 ("r-proxy" ,r-proxy)
2631 ("r-purrr" ,r-purrr)
2634 ("r-rcppparallel" ,r-rcppparallel)
2635 ("r-reshape2" ,r-reshape2)
2636 ("r-reticulate" ,r-reticulate)
2637 ("r-rhpcblasctl" ,r-rhpcblasctl)
2638 ("r-rtsne" ,r-rtsne)
2639 ("r-shiny" ,r-shiny)
2641 ("r-spdep" ,r-spdep)
2642 ("r-speedglm" ,r-speedglm)
2643 ("r-stringr" ,r-stringr)
2644 ("r-singlecellexperiment" ,r-singlecellexperiment)
2645 ("r-tibble" ,r-tibble)
2646 ("r-tidyr" ,r-tidyr)
2648 ("r-viridis" ,r-viridis)))
2649 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2650 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2652 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2653 (license license:expat)))
2655 (define-public r-noiseq
2662 (uri (bioconductor-uri "NOISeq" version))
2665 "1a8p66hhnwmay0rjabwq7356wr93yn33nqgr9rr7whpp9nls1hg4"))))
2666 (properties `((upstream-name . "NOISeq")))
2667 (build-system r-build-system)
2669 `(("r-biobase" ,r-biobase)
2670 ("r-matrix" ,r-matrix)))
2671 (home-page "https://bioconductor.org/packages/NOISeq")
2672 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2674 "This package provides tools to support the analysis of RNA-seq
2675 expression data or other similar kind of data. It provides exploratory plots
2676 to evaluate saturation, count distribution, expression per chromosome, type of
2677 detected features, features length, etc. It also supports the analysis of
2678 differential expression between two experimental conditions with no parametric
2680 (license license:artistic2.0)))
2682 (define-public r-scdd
2689 (uri (bioconductor-uri "scDD" version))
2692 "0nk0qq664zs7dnlcamdkrrhvll01p7f96jj3igbxxlzj3dvr58w4"))))
2693 (properties `((upstream-name . "scDD")))
2694 (build-system r-build-system)
2697 ("r-biocparallel" ,r-biocparallel)
2698 ("r-ebseq" ,r-ebseq)
2699 ("r-fields" ,r-fields)
2700 ("r-ggplot2" ,r-ggplot2)
2701 ("r-mclust" ,r-mclust)
2702 ("r-outliers" ,r-outliers)
2703 ("r-s4vectors" ,r-s4vectors)
2704 ("r-scran" ,r-scran)
2705 ("r-singlecellexperiment" ,r-singlecellexperiment)
2706 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2707 (home-page "https://github.com/kdkorthauer/scDD")
2708 (synopsis "Mixture modeling of single-cell RNA-seq data")
2710 "This package implements a method to analyze single-cell RNA-seq data
2711 utilizing flexible Dirichlet Process mixture models. Genes with differential
2712 distributions of expression are classified into several interesting patterns
2713 of differences between two conditions. The package also includes functions
2714 for simulating data with these patterns from negative binomial
2716 (license license:gpl2)))
2718 (define-public r-scone
2725 (uri (bioconductor-uri "scone" version))
2728 "1hfsbnix0y9ad6bj0d8q2aw13pb3vjcaa0dfwxxapzl90zwbsjhp"))))
2729 (build-system r-build-system)
2731 `(("r-aroma-light" ,r-aroma-light)
2732 ("r-biocparallel" ,r-biocparallel)
2734 ("r-class" ,r-class)
2735 ("r-cluster" ,r-cluster)
2736 ("r-compositions" ,r-compositions)
2737 ("r-diptest" ,r-diptest)
2738 ("r-edger" ,r-edger)
2740 ("r-gplots" ,r-gplots)
2741 ("r-hexbin" ,r-hexbin)
2742 ("r-limma" ,r-limma)
2743 ("r-matrixstats" ,r-matrixstats)
2744 ("r-mixtools" ,r-mixtools)
2745 ("r-rarpack" ,r-rarpack)
2746 ("r-rcolorbrewer" ,r-rcolorbrewer)
2747 ("r-rhdf5" ,r-rhdf5)
2748 ("r-ruvseq" ,r-ruvseq)
2749 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2750 (home-page "https://bioconductor.org/packages/scone")
2751 (synopsis "Single cell overview of normalized expression data")
2753 "SCONE is an R package for comparing and ranking the performance of
2754 different normalization schemes for single-cell RNA-seq and other
2755 high-throughput analyses.")
2756 (license license:artistic2.0)))
2758 (define-public r-geoquery
2765 (uri (bioconductor-uri "GEOquery" version))
2768 "0j8mlldy7dc38fx5zwj6z6l4b9bhvrn8sil3z8asnd4ic7w9ifx5"))))
2769 (properties `((upstream-name . "GEOquery")))
2770 (build-system r-build-system)
2772 `(("r-biobase" ,r-biobase)
2773 ("r-dplyr" ,r-dplyr)
2775 ("r-limma" ,r-limma)
2776 ("r-magrittr" ,r-magrittr)
2777 ("r-readr" ,r-readr)
2778 ("r-tidyr" ,r-tidyr)
2779 ("r-xml2" ,r-xml2)))
2780 (home-page "https://github.com/seandavi/GEOquery/")
2781 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2783 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2784 microarray data. Given the rich and varied nature of this resource, it is
2785 only natural to want to apply BioConductor tools to these data. GEOquery is
2786 the bridge between GEO and BioConductor.")
2787 (license license:gpl2)))
2789 (define-public r-illuminaio
2791 (name "r-illuminaio")
2796 (uri (bioconductor-uri "illuminaio" version))
2799 "1psza8jq6h8fv2rm91ah67dgjlnj1l80yracwgdl1agd0ycv90sh"))))
2800 (build-system r-build-system)
2802 `(("r-base64" ,r-base64)))
2803 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2804 (synopsis "Parse Illumina microarray output files")
2806 "This package provides tools for parsing Illumina's microarray output
2807 files, including IDAT.")
2808 (license license:gpl2)))
2810 (define-public r-siggenes
2817 (uri (bioconductor-uri "siggenes" version))
2820 "03lmq3hqprwps4miynl2vhqi3v4als5vqmz4lb19lk5a4zja72b4"))))
2821 (build-system r-build-system)
2823 `(("r-biobase" ,r-biobase)
2824 ("r-multtest" ,r-multtest)
2825 ("r-scrime" ,r-scrime)))
2826 (home-page "https://bioconductor.org/packages/siggenes/")
2828 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2830 "This package provides tools for the identification of differentially
2831 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2832 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2833 Bayes Analyses of Microarrays} (EBAM).")
2834 (license license:lgpl2.0+)))
2836 (define-public r-bumphunter
2838 (name "r-bumphunter")
2843 (uri (bioconductor-uri "bumphunter" version))
2846 "1p3gwb954zns61d1pwgkplxnvgk2lixrl93kkkf439wa3vlgsnjv"))))
2847 (build-system r-build-system)
2849 `(("r-annotationdbi" ,r-annotationdbi)
2850 ("r-biocgenerics" ,r-biocgenerics)
2851 ("r-dorng" ,r-dorng)
2852 ("r-foreach" ,r-foreach)
2853 ("r-genomeinfodb" ,r-genomeinfodb)
2854 ("r-genomicfeatures" ,r-genomicfeatures)
2855 ("r-genomicranges" ,r-genomicranges)
2856 ("r-iranges" ,r-iranges)
2857 ("r-iterators" ,r-iterators)
2858 ("r-limma" ,r-limma)
2859 ("r-locfit" ,r-locfit)
2860 ("r-matrixstats" ,r-matrixstats)
2861 ("r-s4vectors" ,r-s4vectors)))
2862 (home-page "https://github.com/ririzarr/bumphunter")
2863 (synopsis "Find bumps in genomic data")
2865 "This package provides tools for finding bumps in genomic data in order
2866 to identify differentially methylated regions in epigenetic epidemiology
2868 (license license:artistic2.0)))
2870 (define-public r-minfi
2877 (uri (bioconductor-uri "minfi" version))
2880 "177isdvcq2476xybvfbh7x11qsj5nzckgh3b6p156wlx9ap9dvl3"))))
2881 (build-system r-build-system)
2883 `(("r-beanplot" ,r-beanplot)
2884 ("r-biobase" ,r-biobase)
2885 ("r-biocgenerics" ,r-biocgenerics)
2886 ("r-biocparallel" ,r-biocparallel)
2887 ("r-biostrings" ,r-biostrings)
2888 ("r-bumphunter" ,r-bumphunter)
2889 ("r-data-table" ,r-data-table)
2890 ("r-delayedarray" ,r-delayedarray)
2891 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2892 ("r-genefilter" ,r-genefilter)
2893 ("r-genomeinfodb" ,r-genomeinfodb)
2894 ("r-genomicranges" ,r-genomicranges)
2895 ("r-geoquery" ,r-geoquery)
2896 ("r-hdf5array" ,r-hdf5array)
2897 ("r-illuminaio" ,r-illuminaio)
2898 ("r-iranges" ,r-iranges)
2899 ("r-lattice" ,r-lattice)
2900 ("r-limma" ,r-limma)
2902 ("r-mclust" ,r-mclust)
2904 ("r-nor1mix" ,r-nor1mix)
2905 ("r-preprocesscore" ,r-preprocesscore)
2906 ("r-quadprog" ,r-quadprog)
2907 ("r-rcolorbrewer" ,r-rcolorbrewer)
2908 ("r-reshape" ,r-reshape)
2909 ("r-s4vectors" ,r-s4vectors)
2910 ("r-siggenes" ,r-siggenes)
2911 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2912 (home-page "https://github.com/hansenlab/minfi")
2913 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2915 "This package provides tools to analyze and visualize Illumina Infinium
2916 methylation arrays.")
2917 (license license:artistic2.0)))
2919 (define-public r-methylumi
2921 (name "r-methylumi")
2926 (uri (bioconductor-uri "methylumi" version))
2929 "0zd4h6n37v3z0mas69z2xsf5s0naih828987m8v0g9hhq4f6hf5w"))))
2930 (build-system r-build-system)
2932 `(("r-annotate" ,r-annotate)
2933 ("r-annotationdbi" ,r-annotationdbi)
2934 ("r-biobase" ,r-biobase)
2935 ("r-biocgenerics" ,r-biocgenerics)
2936 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2937 ("r-genefilter" ,r-genefilter)
2938 ("r-genomeinfodb" ,r-genomeinfodb)
2939 ("r-genomicranges" ,r-genomicranges)
2940 ("r-ggplot2" ,r-ggplot2)
2941 ("r-illuminaio" ,r-illuminaio)
2942 ("r-iranges" ,r-iranges)
2943 ("r-lattice" ,r-lattice)
2944 ("r-matrixstats" ,r-matrixstats)
2945 ("r-minfi" ,r-minfi)
2946 ("r-reshape2" ,r-reshape2)
2947 ("r-s4vectors" ,r-s4vectors)
2948 ("r-scales" ,r-scales)
2949 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2950 (home-page "https://bioconductor.org/packages/methylumi")
2951 (synopsis "Handle Illumina methylation data")
2953 "This package provides classes for holding and manipulating Illumina
2954 methylation data. Based on eSet, it can contain MIAME information, sample
2955 information, feature information, and multiple matrices of data. An
2956 \"intelligent\" import function, methylumiR can read the Illumina text files
2957 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2958 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2959 background correction, and quality control features for GoldenGate, Infinium,
2960 and Infinium HD arrays are also included.")
2961 (license license:gpl2)))
2963 (define-public r-lumi
2970 (uri (bioconductor-uri "lumi" version))
2973 "0lgrqbdvp7ykcafc0bpnbcsf396na3jj5c35x9ysf5bpcas23nmm"))))
2974 (build-system r-build-system)
2976 `(("r-affy" ,r-affy)
2977 ("r-annotate" ,r-annotate)
2978 ("r-annotationdbi" ,r-annotationdbi)
2979 ("r-biobase" ,r-biobase)
2981 ("r-genomicfeatures" ,r-genomicfeatures)
2982 ("r-genomicranges" ,r-genomicranges)
2983 ("r-kernsmooth" ,r-kernsmooth)
2984 ("r-lattice" ,r-lattice)
2986 ("r-methylumi" ,r-methylumi)
2988 ("r-nleqslv" ,r-nleqslv)
2989 ("r-preprocesscore" ,r-preprocesscore)
2990 ("r-rsqlite" ,r-rsqlite)))
2991 (home-page "https://bioconductor.org/packages/lumi")
2992 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2994 "The lumi package provides an integrated solution for the Illumina
2995 microarray data analysis. It includes functions of Illumina
2996 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2997 variance stabilization, normalization and gene annotation at the probe level.
2998 It also includes the functions of processing Illumina methylation microarrays,
2999 especially Illumina Infinium methylation microarrays.")
3000 (license license:lgpl2.0+)))
3002 (define-public r-linnorm
3009 (uri (bioconductor-uri "Linnorm" version))
3012 "15mhwiqmp9m65zvrdbr2hhy3x81lf4jbwgjsf75g41if2v2g8x67"))))
3013 (properties `((upstream-name . "Linnorm")))
3014 (build-system r-build-system)
3016 `(("r-amap" ,r-amap)
3017 ("r-apcluster" ,r-apcluster)
3018 ("r-ellipse" ,r-ellipse)
3019 ("r-fastcluster" ,r-fastcluster)
3021 ("r-ggdendro" ,r-ggdendro)
3022 ("r-ggplot2" ,r-ggplot2)
3023 ("r-gmodels" ,r-gmodels)
3024 ("r-igraph" ,r-igraph)
3025 ("r-limma" ,r-limma)
3027 ("r-mclust" ,r-mclust)
3029 ("r-rcpparmadillo" ,r-rcpparmadillo)
3030 ("r-rtsne" ,r-rtsne)
3031 ("r-statmod" ,r-statmod)
3032 ("r-vegan" ,r-vegan)
3034 (home-page "http://www.jjwanglab.org/Linnorm/")
3035 (synopsis "Linear model and normality based transformation method")
3037 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3038 count data or any large scale count data. It transforms such datasets for
3039 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3040 the following pipelines are implemented:
3043 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3044 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3045 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3046 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3047 @item Differential expression analysis or differential peak detection using
3048 limma (@code{Linnorm.limma})
3049 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3050 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3051 @item Stable gene selection for scRNA-seq data; for users without or who do
3052 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3053 @item Data imputation (@code{Linnorm.DataImput}).
3056 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3057 @code{RnaXSim} function is included for simulating RNA-seq data for the
3058 evaluation of DEG analysis methods.")
3059 (license license:expat)))
3061 (define-public r-ioniser
3068 (uri (bioconductor-uri "IONiseR" version))
3071 "1c265bzh923i9mw83mjpj0bzbkixbs6sg1h1z51y9xjkakdgg90f"))))
3072 (properties `((upstream-name . "IONiseR")))
3073 (build-system r-build-system)
3075 `(("r-biocgenerics" ,r-biocgenerics)
3076 ("r-biocparallel" ,r-biocparallel)
3077 ("r-biostrings" ,r-biostrings)
3078 ("r-bit64" ,r-bit64)
3079 ("r-dplyr" ,r-dplyr)
3080 ("r-ggplot2" ,r-ggplot2)
3081 ("r-magrittr" ,r-magrittr)
3082 ("r-rhdf5" ,r-rhdf5)
3083 ("r-shortread" ,r-shortread)
3084 ("r-stringr" ,r-stringr)
3085 ("r-tibble" ,r-tibble)
3086 ("r-tidyr" ,r-tidyr)
3087 ("r-xvector" ,r-xvector)))
3088 (home-page "https://bioconductor.org/packages/IONiseR/")
3089 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3091 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3092 MinION data. It extracts summary statistics from a set of fast5 files and can
3093 be used either before or after base calling. In addition to standard
3094 summaries of the read-types produced, it provides a number of plots for
3095 visualising metrics relative to experiment run time or spatially over the
3096 surface of a flowcell.")
3097 (license license:expat)))
3099 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3100 (define-public r-gkmsvm
3107 (uri (cran-uri "gkmSVM" version))
3110 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
3111 (properties `((upstream-name . "gkmSVM")))
3112 (build-system r-build-system)
3114 `(("r-biocgenerics" ,r-biocgenerics)
3115 ("r-biostrings" ,r-biostrings)
3116 ("r-genomeinfodb" ,r-genomeinfodb)
3117 ("r-genomicranges" ,r-genomicranges)
3118 ("r-iranges" ,r-iranges)
3119 ("r-kernlab" ,r-kernlab)
3122 ("r-rtracklayer" ,r-rtracklayer)
3123 ("r-s4vectors" ,r-s4vectors)
3124 ("r-seqinr" ,r-seqinr)))
3125 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3126 (synopsis "Gapped-kmer support vector machine")
3128 "This R package provides tools for training gapped-kmer SVM classifiers
3129 for DNA and protein sequences. This package supports several sequence
3130 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3131 (license license:gpl2+)))
3133 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
3134 (define-public r-mutoss
3141 (uri (cran-uri "mutoss" version))
3144 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3145 (properties `((upstream-name . "mutoss")))
3146 (build-system r-build-system)
3148 `(("r-multcomp" ,r-multcomp)
3149 ("r-multtest" ,r-multtest)
3150 ("r-mvtnorm" ,r-mvtnorm)
3151 ("r-plotrix" ,r-plotrix)))
3152 (home-page "https://github.com/kornl/mutoss/")
3153 (synopsis "Unified multiple testing procedures")
3155 "This package is designed to ease the application and comparison of
3156 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3157 are standardized and usable by the accompanying mutossGUI package.")
3158 ;; Any version of the GPL.
3159 (license (list license:gpl2+ license:gpl3+))))
3161 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3162 ;; from Bioconductor, so we put it here.
3163 (define-public r-metap
3170 (uri (cran-uri "metap" version))
3173 "0pfbcixjrzx81l9wqhlp55khg9k63zf8pvg2n39c19akr4ppzhvf"))))
3174 (build-system r-build-system)
3176 `(("r-lattice" ,r-lattice)
3177 ("r-mutoss" ,r-mutoss)
3178 ("r-rdpack" ,r-rdpack)
3179 ("r-tfisher" ,r-tfisher)))
3180 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3181 (synopsis "Meta-analysis of significance values")
3183 "The canonical way to perform meta-analysis involves using effect sizes.
3184 When they are not available this package provides a number of methods for
3185 meta-analysis of significance values including the methods of Edgington,
3186 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3187 published results; and a routine for graphical display.")
3188 (license license:gpl2)))
3190 (define-public r-triform
3197 (uri (bioconductor-uri "triform" version))
3200 "12qdyrcw2mcawqdw65v0hjaghzlwa10xl6j8458izcrm5k6dlvz9"))))
3201 (build-system r-build-system)
3203 `(("r-biocgenerics" ,r-biocgenerics)
3204 ("r-iranges" ,r-iranges)
3205 ("r-yaml" ,r-yaml)))
3206 (home-page "https://bioconductor.org/packages/triform/")
3207 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3209 "The Triform algorithm uses model-free statistics to identify peak-like
3210 distributions of TF ChIP sequencing reads, taking advantage of an improved
3211 peak definition in combination with known profile characteristics.")
3212 (license license:gpl2)))
3214 (define-public r-varianttools
3216 (name "r-varianttools")
3221 (uri (bioconductor-uri "VariantTools" version))
3224 "0aafcprsqbn1xl8jqnxfl8r2d0lmzhssqpr26lam2cprh3yk0xiv"))))
3225 (properties `((upstream-name . "VariantTools")))
3226 (build-system r-build-system)
3228 `(("r-biobase" ,r-biobase)
3229 ("r-biocgenerics" ,r-biocgenerics)
3230 ("r-biocparallel" ,r-biocparallel)
3231 ("r-biostrings" ,r-biostrings)
3232 ("r-bsgenome" ,r-bsgenome)
3233 ("r-genomeinfodb" ,r-genomeinfodb)
3234 ("r-genomicfeatures" ,r-genomicfeatures)
3235 ("r-genomicranges" ,r-genomicranges)
3236 ("r-iranges" ,r-iranges)
3237 ("r-matrix" ,r-matrix)
3238 ("r-rsamtools" ,r-rsamtools)
3239 ("r-rtracklayer" ,r-rtracklayer)
3240 ("r-s4vectors" ,r-s4vectors)
3241 ("r-variantannotation" ,r-variantannotation)))
3242 (home-page "https://bioconductor.org/packages/VariantTools/")
3243 (synopsis "Tools for exploratory analysis of variant calls")
3245 "Explore, diagnose, and compare variant calls using filters. The
3246 VariantTools package supports a workflow for loading data, calling single
3247 sample variants and tumor-specific somatic mutations or other sample-specific
3248 variant types (e.g., RNA editing). Most of the functions operate on
3249 alignments (BAM files) or datasets of called variants. The user is expected
3250 to have already aligned the reads with a separate tool, e.g., GSNAP via
3252 (license license:artistic2.0)))
3254 (define-public r-heatplus
3261 (uri (bioconductor-uri "Heatplus" version))
3264 "0hx5gqgh4xrkx37ccprq7azj9jziff137bdk0gvrixcx52ws6h89"))))
3265 (properties `((upstream-name . "Heatplus")))
3266 (build-system r-build-system)
3268 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3269 (home-page "https://github.com/alexploner/Heatplus")
3270 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3272 "This package provides tools to display a rectangular heatmap (intensity
3273 plot) of a data matrix. By default, both samples (columns) and features (row)
3274 of the matrix are sorted according to a hierarchical clustering, and the
3275 corresponding dendrogram is plotted. Optionally, panels with additional
3276 information about samples and features can be added to the plot.")
3277 (license license:gpl2+)))
3279 (define-public r-gosemsim
3286 (uri (bioconductor-uri "GOSemSim" version))
3289 "0pqnlgdvh5szjhwc1mw1snjgpj9lrsnk44bn164cl3zwvdayccya"))))
3290 (properties `((upstream-name . "GOSemSim")))
3291 (build-system r-build-system)
3293 `(("r-annotationdbi" ,r-annotationdbi)
3294 ("r-go-db" ,r-go-db)
3295 ("r-rcpp" ,r-rcpp)))
3296 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3297 (synopsis "GO-terms semantic similarity measures")
3299 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3300 quantitative ways to compute similarities between genes and gene groups, and
3301 have became important basis for many bioinformatics analysis approaches.
3302 GOSemSim is an R package for semantic similarity computation among GO terms,
3303 sets of GO terms, gene products and gene clusters.")
3304 (license license:artistic2.0)))
3306 (define-public r-anota
3313 (uri (bioconductor-uri "anota" version))
3316 "1bkavzrxy1bjz0bwapwa9i3ysln7gljgziwd8c05fmg2f46j1z6m"))))
3317 (build-system r-build-system)
3319 `(("r-multtest" ,r-multtest)
3320 ("r-qvalue" ,r-qvalue)))
3321 (home-page "https://bioconductor.org/packages/anota/")
3322 (synopsis "Analysis of translational activity")
3324 "Genome wide studies of translational control is emerging as a tool to
3325 study various biological conditions. The output from such analysis is both
3326 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3327 involved in translation (the actively translating mRNA level) for each mRNA.
3328 The standard analysis of such data strives towards identifying differential
3329 translational between two or more sample classes - i.e. differences in
3330 actively translated mRNA levels that are independent of underlying differences
3331 in cytosolic mRNA levels. This package allows for such analysis using partial
3332 variances and the random variance model. As 10s of thousands of mRNAs are
3333 analyzed in parallel the library performs a number of tests to assure that
3334 the data set is suitable for such analysis.")
3335 (license license:gpl3)))
3337 (define-public r-sigpathway
3339 (name "r-sigpathway")
3344 (uri (bioconductor-uri "sigPathway" version))
3347 "057qdkbfldpy6hsysk9mrs1vvsqgyl9yx2s6c2f26jz1pardkbqb"))))
3348 (properties `((upstream-name . "sigPathway")))
3349 (build-system r-build-system)
3350 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3351 (synopsis "Pathway analysis")
3353 "This package is used to conduct pathway analysis by calculating the NT_k
3354 and NE_k statistics in a statistical framework for determining whether a
3355 specified group of genes for a pathway has a coordinated association with a
3356 phenotype of interest.")
3357 (license license:gpl2)))
3359 (define-public r-fgsea
3366 (uri (bioconductor-uri "fgsea" version))
3369 "0pbq3g515kcbi4wvfx8m09p01h2f8vwsi1qqsyahxz4r1fasz4c1"))))
3370 (build-system r-build-system)
3373 ("r-biocparallel" ,r-biocparallel)
3374 ("r-data-table" ,r-data-table)
3375 ("r-fastmatch" ,r-fastmatch)
3376 ("r-ggplot2" ,r-ggplot2)
3377 ("r-gridextra" ,r-gridextra)
3378 ("r-matrix" ,r-matrix)
3379 ("r-rcpp" ,r-rcpp)))
3380 (home-page "https://github.com/ctlab/fgsea/")
3381 (synopsis "Fast gene set enrichment analysis")
3383 "The package implements an algorithm for fast gene set enrichment
3384 analysis. Using the fast algorithm allows to make more permutations and get
3385 more fine grained p-values, which allows to use accurate stantard approaches
3386 to multiple hypothesis correction.")
3387 (license license:expat)))
3389 (define-public r-dose
3396 (uri (bioconductor-uri "DOSE" version))
3399 "0ss8mr28q0vswxjmhcas0aqag5nl099jbyn5w3ypbbxqwfvf9jj5"))))
3400 (properties `((upstream-name . "DOSE")))
3401 (build-system r-build-system)
3403 `(("r-annotationdbi" ,r-annotationdbi)
3404 ("r-biocparallel" ,r-biocparallel)
3405 ("r-do-db" ,r-do-db)
3406 ("r-fgsea" ,r-fgsea)
3407 ("r-ggplot2" ,r-ggplot2)
3408 ("r-gosemsim" ,r-gosemsim)
3409 ("r-qvalue" ,r-qvalue)
3410 ("r-reshape2" ,r-reshape2)
3411 ("r-s4vectors" ,r-s4vectors)))
3412 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3413 (synopsis "Disease ontology semantic and enrichment analysis")
3415 "This package implements five methods proposed by Resnik, Schlicker,
3416 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3417 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3418 including hypergeometric model and gene set enrichment analysis are also
3419 implemented for discovering disease associations of high-throughput biological
3421 (license license:artistic2.0)))
3423 (define-public r-enrichplot
3425 (name "r-enrichplot")
3430 (uri (bioconductor-uri "enrichplot" version))
3433 "1jblx00b869xhx1c4n9m2g1hqr00rm9ywr1hrlx42bdd8k5ax1xh"))))
3434 (build-system r-build-system)
3436 `(("r-annotationdbi" ,r-annotationdbi)
3437 ("r-cowplot" ,r-cowplot)
3439 ("r-europepmc" ,r-europepmc)
3440 ("r-ggplot2" ,r-ggplot2)
3441 ("r-ggplotify" ,r-ggplotify)
3442 ("r-ggraph" ,r-ggraph)
3443 ("r-ggridges" ,r-ggridges)
3444 ("r-gosemsim" ,r-gosemsim)
3445 ("r-gridextra" ,r-gridextra)
3446 ("r-igraph" ,r-igraph)
3447 ("r-purrr" ,r-purrr)
3448 ("r-rcolorbrewer" ,r-rcolorbrewer)
3449 ("r-reshape2" ,r-reshape2)))
3450 (home-page "https://github.com/GuangchuangYu/enrichplot")
3451 (synopsis "Visualization of functional enrichment result")
3453 "The enrichplot package implements several visualization methods for
3454 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3455 All the visualization methods are developed based on ggplot2 graphics.")
3456 (license license:artistic2.0)))
3458 (define-public r-clusterprofiler
3460 (name "r-clusterprofiler")
3465 (uri (bioconductor-uri "clusterProfiler" version))
3468 "0mm9iafrsjb8sj27k9mg40ab13vq4rmrzhaajm6g1wdkb2jqikjk"))))
3470 `((upstream-name . "clusterProfiler")))
3471 (build-system r-build-system)
3473 `(("r-annotationdbi" ,r-annotationdbi)
3475 ("r-enrichplot" ,r-enrichplot)
3476 ("r-ggplot2" ,r-ggplot2)
3477 ("r-go-db" ,r-go-db)
3478 ("r-gosemsim" ,r-gosemsim)
3479 ("r-magrittr" ,r-magrittr)
3481 ("r-qvalue" ,r-qvalue)
3482 ("r-rvcheck" ,r-rvcheck)
3483 ("r-tidyr" ,r-tidyr)))
3484 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3485 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3487 "This package implements methods to analyze and visualize functional
3488 profiles (GO and KEGG) of gene and gene clusters.")
3489 (license license:artistic2.0)))
3491 (define-public r-mlinterfaces
3493 (name "r-mlinterfaces")
3498 (uri (bioconductor-uri "MLInterfaces" version))
3501 "1vnzqd3y3jk1wgxybckzrcgwk0ly7zgcz5ki1ib0bk1jwv6xk5x8"))))
3502 (properties `((upstream-name . "MLInterfaces")))
3503 (build-system r-build-system)
3505 `(("r-annotate" ,r-annotate)
3506 ("r-biobase" ,r-biobase)
3507 ("r-biocgenerics" ,r-biocgenerics)
3508 ("r-cluster" ,r-cluster)
3511 ("r-gdata" ,r-gdata)
3512 ("r-genefilter" ,r-genefilter)
3513 ("r-ggvis" ,r-ggvis)
3514 ("r-hwriter" ,r-hwriter)
3516 ("r-mlbench" ,r-mlbench)
3518 ("r-rcolorbrewer" ,r-rcolorbrewer)
3520 ("r-rpart" ,r-rpart)
3521 ("r-sfsmisc" ,r-sfsmisc)
3522 ("r-shiny" ,r-shiny)
3523 ("r-threejs" ,r-threejs)))
3524 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3525 (synopsis "Interfaces to R machine learning procedures")
3527 "This package provides uniform interfaces to machine learning code for
3528 data in R and Bioconductor containers.")
3529 ;; Any version of the LGPL.
3530 (license license:lgpl2.1+)))
3532 (define-public r-annaffy
3539 (uri (bioconductor-uri "annaffy" version))
3542 "1jrf4bq2wky4ay1jrcy60si6hxdcn4j05w5vgs38yfb92gq77i16"))))
3543 (build-system r-build-system)
3546 (modify-phases %standard-phases
3547 (add-after 'unpack 'remove-reference-to-non-free-data
3549 (substitute* "DESCRIPTION"
3553 `(("r-annotationdbi" ,r-annotationdbi)
3554 ("r-biobase" ,r-biobase)
3556 ("r-go-db" ,r-go-db)))
3557 (home-page "https://bioconductor.org/packages/annaffy/")
3558 (synopsis "Annotation tools for Affymetrix biological metadata")
3560 "This package provides functions for handling data from Bioconductor
3561 Affymetrix annotation data packages. It produces compact HTML and text
3562 reports including experimental data and URL links to many online databases.
3563 It allows searching of biological metadata using various criteria.")
3564 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3565 ;; the LGPL 2.1 is included.
3566 (license license:lgpl2.1+)))
3568 (define-public r-a4core
3575 (uri (bioconductor-uri "a4Core" version))
3578 "0xcs9wl2yrprl4yc0z5s4zrkil3752k9xc1fi8fcx7zab1mm80df"))))
3579 (properties `((upstream-name . "a4Core")))
3580 (build-system r-build-system)
3582 `(("r-biobase" ,r-biobase)
3583 ("r-glmnet" ,r-glmnet)))
3584 (home-page "https://bioconductor.org/packages/a4Core")
3585 (synopsis "Automated Affymetrix array analysis core package")
3587 "This is the core package for the automated analysis of Affymetrix
3589 (license license:gpl3)))
3591 (define-public r-a4classif
3593 (name "r-a4classif")
3598 (uri (bioconductor-uri "a4Classif" version))
3601 "0gj3hdflfs1ybc2kshl9w1dzy0rfzppfj08hx3wa2chjsm0m9brn"))))
3602 (properties `((upstream-name . "a4Classif")))
3603 (build-system r-build-system)
3605 `(("r-a4core" ,r-a4core)
3606 ("r-a4preproc" ,r-a4preproc)
3607 ("r-glmnet" ,r-glmnet)
3608 ("r-mlinterfaces" ,r-mlinterfaces)
3611 ("r-varselrf" ,r-varselrf)))
3612 (home-page "https://bioconductor.org/packages/a4Classif/")
3613 (synopsis "Automated Affymetrix array analysis classification package")
3615 "This is the classification package for the automated analysis of
3616 Affymetrix arrays.")
3617 (license license:gpl3)))
3619 (define-public r-a4preproc
3621 (name "r-a4preproc")
3626 (uri (bioconductor-uri "a4Preproc" version))
3629 "11j5nc33gd6yis1fyagr0y39g21bzkc59kq8b8sd6b3pfc84zrjd"))))
3630 (properties `((upstream-name . "a4Preproc")))
3631 (build-system r-build-system)
3633 `(("r-annotationdbi" ,r-annotationdbi)))
3634 (home-page "https://bioconductor.org/packages/a4Preproc/")
3635 (synopsis "Automated Affymetrix array analysis preprocessing package")
3637 "This is a package for the automated analysis of Affymetrix arrays. It
3638 is used for preprocessing the arrays.")
3639 (license license:gpl3)))
3641 (define-public r-a4reporting
3643 (name "r-a4reporting")
3648 (uri (bioconductor-uri "a4Reporting" version))
3651 "15nd4pa5hkdzkhinvqw5ijdqb7k5gk37v2hmk3jsg2d6m0jqphi5"))))
3652 (properties `((upstream-name . "a4Reporting")))
3653 (build-system r-build-system)
3655 `(("r-annaffy" ,r-annaffy)
3656 ("r-xtable" ,r-xtable)))
3657 (home-page "https://bioconductor.org/packages/a4Reporting/")
3658 (synopsis "Automated Affymetrix array analysis reporting package")
3660 "This is a package for the automated analysis of Affymetrix arrays. It
3661 provides reporting features.")
3662 (license license:gpl3)))
3664 (define-public r-a4base
3671 (uri (bioconductor-uri "a4Base" version))
3674 "0dgqyq4dnlcik5qqygnhxlhfr98sh6kmdcj2qllhrwyk0lmsfk01"))))
3675 (properties `((upstream-name . "a4Base")))
3676 (build-system r-build-system)
3678 `(("r-a4core" ,r-a4core)
3679 ("r-a4preproc" ,r-a4preproc)
3680 ("r-annaffy" ,r-annaffy)
3681 ("r-annotationdbi" ,r-annotationdbi)
3682 ("r-biobase" ,r-biobase)
3683 ("r-genefilter" ,r-genefilter)
3684 ("r-glmnet" ,r-glmnet)
3685 ("r-gplots" ,r-gplots)
3686 ("r-limma" ,r-limma)
3688 ("r-multtest" ,r-multtest)))
3689 (home-page "https://bioconductor.org/packages/a4Base/")
3690 (synopsis "Automated Affymetrix array analysis base package")
3692 "This package provides basic features for the automated analysis of
3693 Affymetrix arrays.")
3694 (license license:gpl3)))
3703 (uri (bioconductor-uri "a4" version))
3706 "14yipy6s2wqr9q0yp09x1mm17npknrhs6yd34i3wrb5id64ywnq4"))))
3707 (build-system r-build-system)
3709 `(("r-a4base" ,r-a4base)
3710 ("r-a4classif" ,r-a4classif)
3711 ("r-a4core" ,r-a4core)
3712 ("r-a4preproc" ,r-a4preproc)
3713 ("r-a4reporting" ,r-a4reporting)))
3714 (home-page "https://bioconductor.org/packages/a4/")
3715 (synopsis "Automated Affymetrix array analysis umbrella package")
3717 "This package provides a software suite for the automated analysis of
3718 Affymetrix arrays.")
3719 (license license:gpl3)))
3721 (define-public r-abseqr
3728 (uri (bioconductor-uri "abseqR" version))
3731 "1n9h5qkj4njr1f8fvhg9sj9wxcd7hljnnk8m80zwswzs2n9ivppa"))))
3732 (properties `((upstream-name . "abseqR")))
3733 (build-system r-build-system)
3735 `(("pandoc" ,ghc-pandoc)))
3737 `(("r-biocparallel" ,r-biocparallel)
3738 ("r-biocstyle" ,r-biocstyle)
3739 ("r-circlize" ,r-circlize)
3740 ("r-flexdashboard" ,r-flexdashboard)
3741 ("r-ggcorrplot" ,r-ggcorrplot)
3742 ("r-ggdendro" ,r-ggdendro)
3743 ("r-ggplot2" ,r-ggplot2)
3744 ("r-gridextra" ,r-gridextra)
3745 ("r-knitr" ,r-knitr)
3746 ("r-plotly" ,r-plotly)
3749 ("r-rcolorbrewer" ,r-rcolorbrewer)
3750 ("r-reshape2" ,r-reshape2)
3751 ("r-rmarkdown" ,r-rmarkdown)
3752 ("r-stringr" ,r-stringr)
3753 ("r-vegan" ,r-vegan)
3754 ("r-venndiagram" ,r-venndiagram)))
3755 (home-page "https://github.com/malhamdoosh/abseqR")
3756 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3758 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3759 sequencing datasets generated from antibody libraries and abseqR is one of its
3760 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3761 capabilities and allows them to generate interactive HTML reports for the
3762 convenience of viewing and sharing with other researchers. Additionally,
3763 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3764 further downstream analysis on its output.")
3765 (license license:gpl3)))
3767 (define-public r-bacon
3774 (uri (bioconductor-uri "bacon" version))
3777 "1q18vm4znl47v56cnvx9y5ygrial2mdjpl8x1043jq00kyygrc86"))))
3778 (build-system r-build-system)
3780 `(("r-biocparallel" ,r-biocparallel)
3781 ("r-ellipse" ,r-ellipse)
3782 ("r-ggplot2" ,r-ggplot2)))
3783 (home-page "https://bioconductor.org/packages/bacon/")
3784 (synopsis "Controlling bias and inflation in association studies")
3786 "Bacon can be used to remove inflation and bias often observed in
3787 epigenome- and transcriptome-wide association studies. To this end bacon
3788 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3789 fitting a three-component normal mixture on z-scores.")
3790 (license license:gpl2+)))
3792 (define-public r-rgadem
3799 (uri (bioconductor-uri "rGADEM" version))
3802 "14ylbrzb9haqwfdd9g813mzhll6gwvqf2r7cmbaxz5lkl0j0nglx"))))
3803 (properties `((upstream-name . "rGADEM")))
3804 (build-system r-build-system)
3806 `(("r-biostrings" ,r-biostrings)
3807 ("r-bsgenome" ,r-bsgenome)
3808 ("r-iranges" ,r-iranges)
3809 ("r-seqlogo" ,r-seqlogo)))
3810 (home-page "https://bioconductor.org/packages/rGADEM/")
3811 (synopsis "De novo sequence motif discovery")
3813 "rGADEM is an efficient de novo motif discovery tool for large-scale
3814 genomic sequence data.")
3815 (license license:artistic2.0)))
3817 (define-public r-motiv
3824 (uri (bioconductor-uri "MotIV" version))
3827 "07k4rw4nhcn4sg43psv1h7qr064gws22m2yyr7x8sy3f1i1c954k"))))
3828 (properties `((upstream-name . "MotIV")))
3829 (build-system r-build-system)
3833 `(("r-biocgenerics" ,r-biocgenerics)
3834 ("r-biostrings" ,r-biostrings)
3835 ("r-genomicranges" ,r-genomicranges)
3836 ("r-iranges" ,r-iranges)
3837 ("r-lattice" ,r-lattice)
3838 ("r-rgadem" ,r-rgadem)
3839 ("r-s4vectors" ,r-s4vectors)))
3840 (home-page "https://bioconductor.org/packages/MotIV/")
3841 (synopsis "Motif identification and validation")
3843 "This package is used for the identification and validation of sequence
3844 motifs. It makes use of STAMP for comparing a set of motifs to a given
3845 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3846 distributions, modules and filter motifs.")
3847 (license license:gpl2)))
3849 (define-public r-motifstack
3851 (name "r-motifstack")
3856 (uri (bioconductor-uri "motifStack" version))
3859 "00rafqs1gqlcxlbsdn9qnq9xb7wjphiksb3hsx76viqjbjzi14wg"))))
3860 (properties `((upstream-name . "motifStack")))
3861 (build-system r-build-system)
3863 `(("r-ade4" ,r-ade4)
3864 ("r-biostrings" ,r-biostrings)
3865 ("r-ggplot2" ,r-ggplot2)
3866 ("r-grimport2" ,r-grimport2)
3867 ("r-htmlwidgets" ,r-htmlwidgets)
3868 ("r-motiv" ,r-motiv)
3869 ("r-scales" ,r-scales)
3871 (home-page "https://bioconductor.org/packages/motifStack/")
3872 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3874 "The motifStack package is designed for graphic representation of
3875 multiple motifs with different similarity scores. It works with both DNA/RNA
3876 sequence motifs and amino acid sequence motifs. In addition, it provides the
3877 flexibility for users to customize the graphic parameters such as the font
3878 type and symbol colors.")
3879 (license license:gpl2+)))
3881 (define-public r-genomicscores
3883 (name "r-genomicscores")
3888 (uri (bioconductor-uri "GenomicScores" version))
3891 "175iaqv7npa11yw48vmqpgx0qqs3g44c3dsya7ccwd1lg97fznkj"))))
3892 (properties `((upstream-name . "GenomicScores")))
3893 (build-system r-build-system)
3895 `(("r-annotationhub" ,r-annotationhub)
3896 ("r-biobase" ,r-biobase)
3897 ("r-biocgenerics" ,r-biocgenerics)
3898 ("r-biostrings" ,r-biostrings)
3899 ("r-bsgenome" ,r-bsgenome)
3900 ("r-genomeinfodb" ,r-genomeinfodb)
3901 ("r-genomicranges" ,r-genomicranges)
3902 ("r-iranges" ,r-iranges)
3903 ("r-s4vectors" ,r-s4vectors)
3905 (home-page "https://github.com/rcastelo/GenomicScores/")
3906 (synopsis "Work with genome-wide position-specific scores")
3908 "This package provides infrastructure to store and access genome-wide
3909 position-specific scores within R and Bioconductor.")
3910 (license license:artistic2.0)))
3912 (define-public r-atacseqqc
3914 (name "r-atacseqqc")
3919 (uri (bioconductor-uri "ATACseqQC" version))
3922 "12ix0bvwk50d48z85f3453k7szm1j27gk4qgw56az4fxra472rlh"))))
3923 (properties `((upstream-name . "ATACseqQC")))
3924 (build-system r-build-system)
3926 `(("r-biocgenerics" ,r-biocgenerics)
3927 ("r-biostrings" ,r-biostrings)
3928 ("r-bsgenome" ,r-bsgenome)
3929 ("r-chippeakanno" ,r-chippeakanno)
3930 ("r-edger" ,r-edger)
3931 ("r-genomeinfodb" ,r-genomeinfodb)
3932 ("r-genomicalignments" ,r-genomicalignments)
3933 ("r-genomicranges" ,r-genomicranges)
3934 ("r-genomicscores" ,r-genomicscores)
3935 ("r-iranges" ,r-iranges)
3936 ("r-kernsmooth" ,r-kernsmooth)
3937 ("r-limma" ,r-limma)
3938 ("r-motifstack" ,r-motifstack)
3939 ("r-preseqr" ,r-preseqr)
3940 ("r-randomforest" ,r-randomforest)
3941 ("r-rsamtools" ,r-rsamtools)
3942 ("r-rtracklayer" ,r-rtracklayer)
3943 ("r-s4vectors" ,r-s4vectors)))
3944 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3945 (synopsis "ATAC-seq quality control")
3947 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3948 sequencing, is a rapid and sensitive method for chromatin accessibility
3949 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3950 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3951 assess whether their ATAC-seq experiment is successful. It includes
3952 diagnostic plots of fragment size distribution, proportion of mitochondria
3953 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3955 (license license:gpl2+)))
3957 (define-public r-gofuncr
3964 (uri (bioconductor-uri "GOfuncR" version))
3967 "0hmi13pz923fm95asys615rih63b1i2nvynfczr1zcsc9fzn4h35"))))
3968 (properties `((upstream-name . "GOfuncR")))
3969 (build-system r-build-system)
3971 `(("r-annotationdbi" ,r-annotationdbi)
3972 ("r-genomicranges" ,r-genomicranges)
3973 ("r-gtools" ,r-gtools)
3974 ("r-iranges" ,r-iranges)
3975 ("r-mapplots" ,r-mapplots)
3977 ("r-vioplot" ,r-vioplot)))
3978 (home-page "https://bioconductor.org/packages/GOfuncR/")
3979 (synopsis "Gene ontology enrichment using FUNC")
3981 "GOfuncR performs a gene ontology enrichment analysis based on the
3982 ontology enrichment software FUNC. GO-annotations are obtained from
3983 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3984 included in the package and updated regularly. GOfuncR provides the standard
3985 candidate vs background enrichment analysis using the hypergeometric test, as
3986 well as three additional tests:
3989 @item the Wilcoxon rank-sum test that is used when genes are ranked,
3990 @item a binomial test that is used when genes are associated with two counts,
3992 @item a Chi-square or Fisher's exact test that is used in cases when genes are
3993 associated with four counts.
3996 To correct for multiple testing and interdependency of the tests, family-wise
3997 error rates are computed based on random permutations of the gene-associated
3998 variables. GOfuncR also provides tools for exploring the ontology graph and
3999 the annotations, and options to take gene-length or spatial clustering of
4000 genes into account. It is also possible to provide custom gene coordinates,
4001 annotations and ontologies.")
4002 (license license:gpl2+)))
4004 (define-public r-abaenrichment
4006 (name "r-abaenrichment")
4011 (uri (bioconductor-uri "ABAEnrichment" version))
4014 "128ik28j8kmdkycffhxajv5h174zdq9sfn2gz6ai90wgkdadbzwp"))))
4015 (properties `((upstream-name . "ABAEnrichment")))
4016 (build-system r-build-system)
4018 `(("r-abadata" ,r-abadata)
4019 ("r-data-table" ,r-data-table)
4020 ("r-gofuncr" ,r-gofuncr)
4021 ("r-gplots" ,r-gplots)
4022 ("r-gtools" ,r-gtools)
4023 ("r-rcpp" ,r-rcpp)))
4024 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4025 (synopsis "Gene expression enrichment in human brain regions")
4027 "The package ABAEnrichment is designed to test for enrichment of user
4028 defined candidate genes in the set of expressed genes in different human brain
4029 regions. The core function @code{aba_enrich} integrates the expression of the
4030 candidate gene set (averaged across donors) and the structural information of
4031 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4032 (license license:gpl2+)))
4034 (define-public r-annotationfuncs
4036 (name "r-annotationfuncs")
4041 (uri (bioconductor-uri "AnnotationFuncs" version))
4044 "0ws14b1ibqml7w8kj0gi7wdp6wd8dcdpnrmcxldjzsyawf17q0yq"))))
4046 `((upstream-name . "AnnotationFuncs")))
4047 (build-system r-build-system)
4049 `(("r-annotationdbi" ,r-annotationdbi)
4051 (home-page "https://www.iysik.com/r/annotationfuncs")
4052 (synopsis "Annotation translation functions")
4054 "This package provides functions for handling translating between
4055 different identifieres using the Biocore Data Team data-packages (e.g.
4056 @code{org.Bt.eg.db}).")
4057 (license license:gpl2)))
4059 (define-public r-annotationtools
4061 (name "r-annotationtools")
4066 (uri (bioconductor-uri "annotationTools" version))
4069 "1cq7ayq2swp2ahlphz74nh5mb869rgyyr0kkqy1mxyilk8k2g44i"))))
4071 `((upstream-name . "annotationTools")))
4072 (build-system r-build-system)
4073 (propagated-inputs `(("r-biobase" ,r-biobase)))
4074 (home-page "https://bioconductor.org/packages/annotationTools/")
4075 (synopsis "Annotate microarrays and perform gene expression analyses")
4077 "This package provides functions to annotate microarrays, find orthologs,
4078 and integrate heterogeneous gene expression profiles using annotation and
4079 other molecular biology information available as flat file database (plain
4081 ;; Any version of the GPL.
4082 (license (list license:gpl2+))))
4084 (define-public r-allelicimbalance
4086 (name "r-allelicimbalance")
4091 (uri (bioconductor-uri "AllelicImbalance" version))
4094 "0vy8w7ii2qljsmq8lr21lygkcrsshc7syyqhadlbxyj3scgi7kyc"))))
4096 `((upstream-name . "AllelicImbalance")))
4097 (build-system r-build-system)
4099 `(("r-annotationdbi" ,r-annotationdbi)
4100 ("r-biocgenerics" ,r-biocgenerics)
4101 ("r-biostrings" ,r-biostrings)
4102 ("r-bsgenome" ,r-bsgenome)
4103 ("r-genomeinfodb" ,r-genomeinfodb)
4104 ("r-genomicalignments" ,r-genomicalignments)
4105 ("r-genomicfeatures" ,r-genomicfeatures)
4106 ("r-genomicranges" ,r-genomicranges)
4107 ("r-gridextra" ,r-gridextra)
4109 ("r-iranges" ,r-iranges)
4110 ("r-lattice" ,r-lattice)
4111 ("r-latticeextra" ,r-latticeextra)
4113 ("r-rsamtools" ,r-rsamtools)
4114 ("r-s4vectors" ,r-s4vectors)
4115 ("r-seqinr" ,r-seqinr)
4116 ("r-summarizedexperiment" ,r-summarizedexperiment)
4117 ("r-variantannotation" ,r-variantannotation)))
4118 (home-page "https://github.com/pappewaio/AllelicImbalance")
4119 (synopsis "Investigate allele-specific expression")
4121 "This package provides a framework for allele-specific expression
4122 investigation using RNA-seq data.")
4123 (license license:gpl3)))
4125 (define-public r-aucell
4132 (uri (bioconductor-uri "AUCell" version))
4135 "1g4mdq8z29fjxrfjng0fb3cvbph49mwds4ijsa2bn2k6f75dnzky"))))
4136 (properties `((upstream-name . "AUCell")))
4137 (build-system r-build-system)
4139 `(("r-biocgenerics" ,r-biocgenerics)
4140 ("r-data-table" ,r-data-table)
4141 ("r-gseabase" ,r-gseabase)
4142 ("r-mixtools" ,r-mixtools)
4143 ("r-r-utils" ,r-r-utils)
4144 ("r-s4vectors" ,r-s4vectors)
4145 ("r-shiny" ,r-shiny)
4146 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4147 (home-page "https://bioconductor.org/packages/AUCell/")
4148 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4150 "AUCell allows to identify cells with active gene sets (e.g. signatures,
4151 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4152 Under the Curve} (AUC) to calculate whether a critical subset of the input
4153 gene set is enriched within the expressed genes for each cell. The
4154 distribution of AUC scores across all the cells allows exploring the relative
4155 expression of the signature. Since the scoring method is ranking-based,
4156 AUCell is independent of the gene expression units and the normalization
4157 procedure. In addition, since the cells are evaluated individually, it can
4158 easily be applied to bigger datasets, subsetting the expression matrix if
4160 (license license:gpl3)))
4162 (define-public r-ebimage
4169 (uri (bioconductor-uri "EBImage" version))
4172 "0q54q2nw6p1s4nrj1l8qz78m67xcysj2x82zs43my8iv2g9iifgs"))))
4173 (properties `((upstream-name . "EBImage")))
4174 (build-system r-build-system)
4176 `(("r-abind" ,r-abind)
4177 ("r-biocgenerics" ,r-biocgenerics)
4178 ("r-fftwtools" ,r-fftwtools)
4179 ("r-htmltools" ,r-htmltools)
4180 ("r-htmlwidgets" ,r-htmlwidgets)
4182 ("r-locfit" ,r-locfit)
4184 ("r-rcurl" ,r-rcurl)
4185 ("r-tiff" ,r-tiff)))
4187 `(("r-knitr" ,r-knitr))) ; for vignettes
4188 (home-page "https://github.com/aoles/EBImage")
4189 (synopsis "Image processing and analysis toolbox for R")
4191 "EBImage provides general purpose functionality for image processing and
4192 analysis. In the context of (high-throughput) microscopy-based cellular
4193 assays, EBImage offers tools to segment cells and extract quantitative
4194 cellular descriptors. This allows the automation of such tasks using the R
4195 programming language and facilitates the use of other tools in the R
4196 environment for signal processing, statistical modeling, machine learning and
4197 visualization with image data.")
4198 ;; Any version of the LGPL.
4199 (license license:lgpl2.1+)))
4201 (define-public r-yamss
4208 (uri (bioconductor-uri "yamss" version))
4211 "1n49a2vg1667wycrjww29xfafngllvpb5nq5wy6pgn0akva91nky"))))
4212 (build-system r-build-system)
4214 `(("r-biocgenerics" ,r-biocgenerics)
4215 ("r-data-table" ,r-data-table)
4216 ("r-ebimage" ,r-ebimage)
4217 ("r-iranges" ,r-iranges)
4218 ("r-limma" ,r-limma)
4219 ("r-matrix" ,r-matrix)
4221 ("r-s4vectors" ,r-s4vectors)
4222 ("r-summarizedexperiment"
4223 ,r-summarizedexperiment)))
4224 (home-page "https://github.com/hansenlab/yamss")
4225 (synopsis "Tools for high-throughput metabolomics")
4227 "This package provides tools to analyze and visualize high-throughput
4228 metabolomics data acquired using chromatography-mass spectrometry. These tools
4229 preprocess data in a way that enables reliable and powerful differential
4231 (license license:artistic2.0)))
4233 (define-public r-gtrellis
4240 (uri (bioconductor-uri "gtrellis" version))
4243 "0mgspmv6p1a2k98jyy2dfl0wpa2vh7bhnjfm2xaqmcsxzmbjhh9z"))))
4244 (build-system r-build-system)
4246 `(("r-circlize" ,r-circlize)
4247 ("r-genomicranges" ,r-genomicranges)
4248 ("r-getoptlong" ,r-getoptlong)
4249 ("r-iranges" ,r-iranges)))
4250 (home-page "https://github.com/jokergoo/gtrellis")
4251 (synopsis "Genome level Trellis layout")
4253 "Genome level Trellis graph visualizes genomic data conditioned by
4254 genomic categories (e.g. chromosomes). For each genomic category, multiple
4255 dimensional data which are represented as tracks describe different features
4256 from different aspects. This package provides high flexibility to arrange
4257 genomic categories and to add self-defined graphics in the plot.")
4258 (license license:expat)))
4260 (define-public r-somaticsignatures
4262 (name "r-somaticsignatures")
4267 (uri (bioconductor-uri "SomaticSignatures" version))
4270 "1gvrkahllwz38g3hn9pjlikhfqz19a4qglcqmyrxk7h9ybx5zy5z"))))
4272 `((upstream-name . "SomaticSignatures")))
4273 (build-system r-build-system)
4275 `(("r-biobase" ,r-biobase)
4276 ("r-biostrings" ,r-biostrings)
4277 ("r-genomeinfodb" ,r-genomeinfodb)
4278 ("r-genomicranges" ,r-genomicranges)
4279 ("r-ggbio" ,r-ggbio)
4280 ("r-ggplot2" ,r-ggplot2)
4281 ("r-iranges" ,r-iranges)
4283 ("r-pcamethods" ,r-pcamethods)
4284 ("r-proxy" ,r-proxy)
4285 ("r-reshape2" ,r-reshape2)
4286 ("r-s4vectors" ,r-s4vectors)
4287 ("r-variantannotation" ,r-variantannotation)))
4288 (home-page "https://github.com/juliangehring/SomaticSignatures")
4289 (synopsis "Somatic signatures")
4291 "This package identifies mutational signatures of @dfn{single nucleotide
4292 variants} (SNVs). It provides a infrastructure related to the methodology
4293 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4294 decomposition algorithms.")
4295 (license license:expat)))
4297 (define-public r-yapsa
4304 (uri (bioconductor-uri "YAPSA" version))
4307 "132x51f8k8zyx6j8jk05x4lr9q1hlblgvr69wkhn0q3f8mhaj926"))))
4308 (properties `((upstream-name . "YAPSA")))
4309 (build-system r-build-system)
4311 `(("r-circlize" ,r-circlize)
4312 ("r-complexheatmap" ,r-complexheatmap)
4313 ("r-corrplot" ,r-corrplot)
4314 ("r-dendextend" ,r-dendextend)
4315 ("r-genomeinfodb" ,r-genomeinfodb)
4316 ("r-genomicranges" ,r-genomicranges)
4317 ("r-getoptlong" ,r-getoptlong)
4318 ("r-ggplot2" ,r-ggplot2)
4319 ("r-gridextra" ,r-gridextra)
4320 ("r-gtrellis" ,r-gtrellis)
4321 ("r-keggrest" ,r-keggrest)
4323 ("r-pmcmr" ,r-pmcmr)
4324 ("r-reshape2" ,r-reshape2)
4325 ("r-somaticsignatures" ,r-somaticsignatures)
4326 ("r-variantannotation" ,r-variantannotation)))
4327 (home-page "https://bioconductor.org/packages/YAPSA/")
4328 (synopsis "Yet another package for signature analysis")
4330 "This package provides functions and routines useful in the analysis of
4331 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4332 functions to perform a signature analysis with known signatures and a
4333 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4335 (license license:gpl3)))
4337 (define-public r-gcrma
4344 (uri (bioconductor-uri "gcrma" version))
4347 "0c9sa9ldlcpdcjdan8m4ndnyaisr6wbarq486sl44ikh7wf1csfx"))))
4348 (build-system r-build-system)
4350 `(("r-affy" ,r-affy)
4351 ("r-affyio" ,r-affyio)
4352 ("r-biobase" ,r-biobase)
4353 ("r-biocmanager" ,r-biocmanager)
4354 ("r-biostrings" ,r-biostrings)
4355 ("r-xvector" ,r-xvector)))
4356 (home-page "https://bioconductor.org/packages/gcrma/")
4357 (synopsis "Background adjustment using sequence information")
4359 "Gcrma adjusts for background intensities in Affymetrix array data which
4360 include optical noise and @dfn{non-specific binding} (NSB). The main function
4361 @code{gcrma} converts background adjusted probe intensities to expression
4362 measures using the same normalization and summarization methods as a
4363 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4364 to estimate probe affinity to NSB. The sequence information is summarized in
4365 a more complex way than the simple GC content. Instead, the base types (A, T,
4366 G or C) at each position along the probe determine the affinity of each probe.
4367 The parameters of the position-specific base contributions to the probe
4368 affinity is estimated in an NSB experiment in which only NSB but no
4369 gene-specific bidning is expected.")
4370 ;; Any version of the LGPL
4371 (license license:lgpl2.1+)))
4373 (define-public r-simpleaffy
4375 (name "r-simpleaffy")
4380 (uri (bioconductor-uri "simpleaffy" version))
4383 "18bz3pfgp0f7906flrljx97ann8s71pnb8gpw7nah46n8vqc0xcs"))))
4384 (build-system r-build-system)
4386 `(("r-affy" ,r-affy)
4387 ("r-biobase" ,r-biobase)
4388 ("r-biocgenerics" ,r-biocgenerics)
4389 ("r-gcrma" ,r-gcrma)
4390 ("r-genefilter" ,r-genefilter)))
4391 (home-page "https://bioconductor.org/packages/simpleaffy/")
4392 (synopsis "Very simple high level analysis of Affymetrix data")
4394 "This package provides high level functions for reading Affy @file{.CEL}
4395 files, phenotypic data, and then computing simple things with it, such as
4396 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4397 library. It also has some basic scatter plot functions and mechanisms for
4398 generating high resolution journal figures.")
4399 (license license:gpl2+)))
4401 (define-public r-yaqcaffy
4408 (uri (bioconductor-uri "yaqcaffy" version))
4411 "0kzzqsf1lfbcmy95w2z0c9qrvp7mbwm50k2l9wvz3xa5wz6xa7gz"))))
4412 (build-system r-build-system)
4414 `(("r-simpleaffy" ,r-simpleaffy)))
4415 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4416 (synopsis "Affymetrix quality control and reproducibility analysis")
4418 "This is a package that can be used for quality control of Affymetrix
4419 GeneChip expression data and reproducibility analysis of human whole genome
4420 chips with the MAQC reference datasets.")
4421 (license license:artistic2.0)))
4423 (define-public r-quantro
4430 (uri (bioconductor-uri "quantro" version))
4433 "09f3x1j50ll5hhn3qwys5x06mii3fqsrk6dkvsxai0kdxv9cjz9m"))))
4434 (build-system r-build-system)
4436 `(("r-biobase" ,r-biobase)
4437 ("r-doparallel" ,r-doparallel)
4438 ("r-foreach" ,r-foreach)
4439 ("r-ggplot2" ,r-ggplot2)
4440 ("r-iterators" ,r-iterators)
4441 ("r-minfi" ,r-minfi)
4442 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4443 (home-page "https://bioconductor.org/packages/quantro/")
4444 (synopsis "Test for when to use quantile normalization")
4446 "This package provides a data-driven test for the assumptions of quantile
4447 normalization using raw data such as objects that inherit eSets (e.g.
4448 ExpressionSet, MethylSet). Group level information about each sample (such as
4449 Tumor / Normal status) must also be provided because the test assesses if
4450 there are global differences in the distributions between the user-defined
4452 (license license:gpl3+)))
4454 (define-public r-yarn
4461 (uri (bioconductor-uri "yarn" version))
4464 "0891a10adkhm1zpm7fpcxc2xfxjf9yrpckaz87b2wdjdiwivc4cp"))))
4465 (build-system r-build-system)
4467 `(("r-biobase" ,r-biobase)
4468 ("r-biomart" ,r-biomart)
4469 ("r-downloader" ,r-downloader)
4470 ("r-edger" ,r-edger)
4471 ("r-gplots" ,r-gplots)
4472 ("r-limma" ,r-limma)
4473 ("r-matrixstats" ,r-matrixstats)
4474 ("r-preprocesscore" ,r-preprocesscore)
4475 ("r-quantro" ,r-quantro)
4476 ("r-rcolorbrewer" ,r-rcolorbrewer)
4477 ("r-readr" ,r-readr)))
4478 (home-page "https://bioconductor.org/packages/yarn/")
4479 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4481 "Expedite large RNA-Seq analyses using a combination of previously
4482 developed tools. YARN is meant to make it easier for the user in performing
4483 basic mis-annotation quality control, filtering, and condition-aware
4484 normalization. YARN leverages many Bioconductor tools and statistical
4485 techniques to account for the large heterogeneity and sparsity found in very
4486 large RNA-seq experiments.")
4487 (license license:artistic2.0)))
4489 (define-public r-roar
4496 (uri (bioconductor-uri "roar" version))
4499 "1nqw0agx9x8ycdf0gw17fdlnmzpw9x3zig1wcy10xpyhyjdbbi06"))))
4500 (build-system r-build-system)
4502 `(("r-biocgenerics" ,r-biocgenerics)
4503 ("r-genomeinfodb" ,r-genomeinfodb)
4504 ("r-genomicalignments" ,r-genomicalignments)
4505 ("r-genomicranges" ,r-genomicranges)
4506 ("r-iranges" ,r-iranges)
4507 ("r-rtracklayer" ,r-rtracklayer)
4508 ("r-s4vectors" ,r-s4vectors)
4509 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4510 (home-page "https://github.com/vodkatad/roar/")
4511 (synopsis "Identify differential APA usage from RNA-seq alignments")
4513 "This package provides tools for identifying preferential usage of APA
4514 sites, comparing two biological conditions, starting from known alternative
4515 sites and alignments obtained from standard RNA-seq experiments.")
4516 (license license:gpl3)))
4518 (define-public r-xbseq
4525 (uri (bioconductor-uri "XBSeq" version))
4528 "1qr5gvf8jcx6r0ac7d2wmnikswmp3k71lirnw7dyr6fndzrdz9lp"))))
4529 (properties `((upstream-name . "XBSeq")))
4530 (build-system r-build-system)
4532 `(("r-biobase" ,r-biobase)
4533 ("r-deseq2" ,r-deseq2)
4534 ("r-dplyr" ,r-dplyr)
4535 ("r-ggplot2" ,r-ggplot2)
4536 ("r-locfit" ,r-locfit)
4537 ("r-magrittr" ,r-magrittr)
4538 ("r-matrixstats" ,r-matrixstats)
4539 ("r-pracma" ,r-pracma)
4540 ("r-roar" ,r-roar)))
4541 (home-page "https://github.com/Liuy12/XBSeq")
4542 (synopsis "Test for differential expression for RNA-seq data")
4544 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4545 expression} (DE), where a statistical model was established based on the
4546 assumption that observed signals are the convolution of true expression
4547 signals and sequencing noises. The mapped reads in non-exonic regions are
4548 considered as sequencing noises, which follows a Poisson distribution. Given
4549 measurable observed signal and background noise from RNA-seq data, true
4550 expression signals, assuming governed by the negative binomial distribution,
4551 can be delineated and thus the accurate detection of differential expressed
4553 (license license:gpl3+)))
4555 (define-public r-massspecwavelet
4557 (name "r-massspecwavelet")
4562 (uri (bioconductor-uri "MassSpecWavelet" version))
4565 "0xnj3ncrwvr2b8msi3g77mgzj0zaksn3lgqdn1abh0ww5wgk83v7"))))
4567 `((upstream-name . "MassSpecWavelet")))
4568 (build-system r-build-system)
4570 `(("r-waveslim" ,r-waveslim)))
4571 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4572 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4574 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4575 data mainly through the use of wavelet transforms. It supports peak detection
4576 based on @dfn{Continuous Wavelet Transform} (CWT).")
4577 (license license:lgpl2.0+)))
4579 (define-public r-xcms
4586 (uri (bioconductor-uri "xcms" version))
4589 "18iglvlvlxrdwn2apdvihj9jxmx0kwm5z37rml67xcj9sfdi3bjb"))))
4590 (build-system r-build-system)
4592 `(("r-biobase" ,r-biobase)
4593 ("r-biocgenerics" ,r-biocgenerics)
4594 ("r-biocparallel" ,r-biocparallel)
4595 ("r-iranges" ,r-iranges)
4596 ("r-lattice" ,r-lattice)
4597 ("r-massspecwavelet" ,r-massspecwavelet)
4598 ("r-msnbase" ,r-msnbase)
4599 ("r-multtest" ,r-multtest)
4602 ("r-protgenerics" ,r-protgenerics)
4604 ("r-rcolorbrewer" ,r-rcolorbrewer)
4605 ("r-robustbase" ,r-robustbase)
4606 ("r-s4vectors" ,r-s4vectors)))
4607 (home-page "https://bioconductor.org/packages/xcms/")
4608 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4610 "This package provides a framework for processing and visualization of
4611 chromatographically separated and single-spectra mass spectral data. It
4612 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4613 data for high-throughput, untargeted analyte profiling.")
4614 (license license:gpl2+)))
4616 (define-public r-wrench
4623 (uri (bioconductor-uri "Wrench" version))
4626 "1s8d7jn0dk5zk2fhvsd4sgicypz4c41nzf19nqzcwb9bd6asgrwm"))))
4627 (properties `((upstream-name . "Wrench")))
4628 (build-system r-build-system)
4630 `(("r-limma" ,r-limma)
4631 ("r-locfit" ,r-locfit)
4632 ("r-matrixstats" ,r-matrixstats)))
4633 (home-page "https://github.com/HCBravoLab/Wrench")
4634 (synopsis "Wrench normalization for sparse count data")
4636 "Wrench is a package for normalization sparse genomic count data, like
4637 that arising from 16s metagenomic surveys.")
4638 (license license:artistic2.0)))
4640 (define-public r-wiggleplotr
4642 (name "r-wiggleplotr")
4647 (uri (bioconductor-uri "wiggleplotr" version))
4650 "1pj2bsn5azs18mp5hr4g7c6rnds2y2rjjnak2785kaj7xi8jly4m"))))
4651 (build-system r-build-system)
4653 `(("r-assertthat" ,r-assertthat)
4654 ("r-cowplot" ,r-cowplot)
4655 ("r-dplyr" ,r-dplyr)
4656 ("r-genomeinfodb" ,r-genomeinfodb)
4657 ("r-genomicranges" ,r-genomicranges)
4658 ("r-ggplot2" ,r-ggplot2)
4659 ("r-iranges" ,r-iranges)
4660 ("r-purrr" ,r-purrr)
4661 ("r-rtracklayer" ,r-rtracklayer)
4662 ("r-s4vectors" ,r-s4vectors)))
4663 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4664 (synopsis "Make read coverage plots from BigWig files")
4666 "This package provides tools to visualize read coverage from sequencing
4667 experiments together with genomic annotations (genes, transcripts, peaks).
4668 Introns of long transcripts can be rescaled to a fixed length for better
4669 visualization of exonic read coverage.")
4670 (license license:asl2.0)))
4672 (define-public r-widgettools
4674 (name "r-widgettools")
4679 (uri (bioconductor-uri "widgetTools" version))
4682 "1nqy3icayacv5mlv5s5xgfli0dqzancs6zpffrl5p237c994nyr5"))))
4683 (properties `((upstream-name . "widgetTools")))
4684 (build-system r-build-system)
4685 (home-page "https://bioconductor.org/packages/widgetTools/")
4686 (synopsis "Tools for creating interactive tcltk widgets")
4688 "This package contains tools to support the construction of tcltk
4690 ;; Any version of the LGPL.
4691 (license license:lgpl3+)))
4693 (define-public r-webbioc
4700 (uri (bioconductor-uri "webbioc" version))
4703 "1cwrmvh1l603k6j1r425c4vrqp0zf0x7bgx7y1wnbq4r7yc5sp62"))))
4704 (build-system r-build-system)
4706 `(("netpbm" ,netpbm)
4709 `(("r-affy" ,r-affy)
4710 ("r-annaffy" ,r-annaffy)
4711 ("r-biobase" ,r-biobase)
4712 ("r-biocmanager" ,r-biocmanager)
4713 ("r-gcrma" ,r-gcrma)
4714 ("r-multtest" ,r-multtest)
4715 ("r-qvalue" ,r-qvalue)
4717 (home-page "https://www.bioconductor.org/")
4718 (synopsis "Bioconductor web interface")
4720 "This package provides an integrated web interface for doing microarray
4721 analysis using several of the Bioconductor packages. It is intended to be
4722 deployed as a centralized bioinformatics resource for use by many users.
4723 Currently only Affymetrix oligonucleotide analysis is supported.")
4724 (license license:gpl2+)))
4726 (define-public r-zfpkm
4733 (uri (bioconductor-uri "zFPKM" version))
4736 "1hg0vc0ns8d4jpddn1v5a5m13a033b0wf1al01pb1lvmx5mzzr2n"))))
4737 (properties `((upstream-name . "zFPKM")))
4738 (build-system r-build-system)
4740 `(("r-checkmate" ,r-checkmate)
4741 ("r-dplyr" ,r-dplyr)
4742 ("r-ggplot2" ,r-ggplot2)
4743 ("r-summarizedexperiment" ,r-summarizedexperiment)
4744 ("r-tidyr" ,r-tidyr)))
4745 (home-page "https://github.com/ronammar/zFPKM/")
4746 (synopsis "Functions to facilitate zFPKM transformations")
4748 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
4749 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
4751 (license license:gpl3)))
4753 (define-public r-rbowtie2
4760 (uri (bioconductor-uri "Rbowtie2" version))
4763 "1b7x42n9zisi2w2wwfc0c39j8s9868imyr0ysqgswf6l5mv9ivc5"))))
4764 (properties `((upstream-name . "Rbowtie2")))
4765 (build-system r-build-system)
4768 (home-page "https://bioconductor.org/packages/Rbowtie2/")
4769 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
4771 "This package provides an R wrapper of the popular @code{bowtie2}
4772 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
4773 rapid adapter trimming, identification, and read merging.")
4774 (license license:gpl3+)))
4776 (define-public r-progeny
4783 (uri (bioconductor-uri "progeny" version))
4786 "0j3kxjj7xmmwb29p87n3bw7bl38gcb94jrpw32126a578rf1pfrq"))))
4787 (build-system r-build-system)
4788 (propagated-inputs `(("r-biobase" ,r-biobase)))
4789 (home-page "https://github.com/saezlab/progeny")
4790 (synopsis "Pathway responsive gene activity inference")
4792 "This package provides a function to infer pathway activity from gene
4793 expression. It contains the linear model inferred in the publication
4794 \"Perturbation-response genes reveal signaling footprints in cancer gene
4796 (license license:asl2.0)))
4798 (define-public r-arrmnormalization
4800 (name "r-arrmnormalization")
4805 (uri (bioconductor-uri "ARRmNormalization" version))
4808 "0jj81q454nyh4hr5c56q1hv7i4ynx3rwnvpv08w34a6m77122bi1"))))
4810 `((upstream-name . "ARRmNormalization")))
4811 (build-system r-build-system)
4812 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
4813 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
4814 (synopsis "Adaptive robust regression normalization for methylation data")
4816 "This is a package to perform the @dfn{Adaptive Robust Regression
4817 method} (ARRm) for the normalization of methylation data from the Illumina
4818 Infinium HumanMethylation 450k assay.")
4819 (license license:artistic2.0)))
4821 (define-public r-biocfilecache
4823 (name "r-biocfilecache")
4828 (uri (bioconductor-uri "BiocFileCache" version))
4831 "0jivhn95y6zv5ryamqk6nyd4l8nlskq64j362l9ml9qw746v0ja6"))))
4832 (properties `((upstream-name . "BiocFileCache")))
4833 (build-system r-build-system)
4835 `(("r-curl" ,r-curl)
4837 ("r-dbplyr" ,r-dbplyr)
4838 ("r-dplyr" ,r-dplyr)
4840 ("r-rappdirs" ,r-rappdirs)
4841 ("r-rsqlite" ,r-rsqlite)))
4842 (home-page "https://bioconductor.org/packages/BiocFileCache/")
4843 (synopsis "Manage files across sessions")
4845 "This package creates a persistent on-disk cache of files that the user
4846 can add, update, and retrieve. It is useful for managing resources (such as
4847 custom Txdb objects) that are costly or difficult to create, web resources,
4848 and data files used across sessions.")
4849 (license license:artistic2.0)))
4851 (define-public r-iclusterplus
4853 (name "r-iclusterplus")
4858 (uri (bioconductor-uri "iClusterPlus" version))
4861 "1dzgfzf2x8m62hssvsn1zzag7m444kyxj2vpdxl9nk859dr5pf37"))))
4862 (properties `((upstream-name . "iClusterPlus")))
4863 (build-system r-build-system)
4864 (native-inputs `(("gfortran" ,gfortran)))
4865 (home-page "https://bioconductor.org/packages/iClusterPlus/")
4866 (synopsis "Integrative clustering of multi-type genomic data")
4868 "iClusterPlus is developed for integrative clustering analysis of
4869 multi-type genomic data and is an enhanced version of iCluster proposed and
4870 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
4871 from the experiments where biological samples (e.g. tumor samples) are
4872 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
4873 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
4874 on. In the iClusterPlus model, binary observations such as somatic mutation
4875 are modeled as Binomial processes; categorical observations such as copy
4876 number states are realizations of Multinomial random variables; counts are
4877 modeled as Poisson random processes; and continuous measures are modeled by
4878 Gaussian distributions.")
4879 (license license:gpl2+)))
4881 (define-public r-rbowtie
4888 (uri (bioconductor-uri "Rbowtie" version))
4891 "0yy31xhdmf6xb21wlhmxxwfqpm0nil39pb2cs3pq5ia758lb88z4"))))
4892 (properties `((upstream-name . "Rbowtie")))
4893 (build-system r-build-system)
4896 (home-page "https://bioconductor.org/packages/Rbowtie/")
4897 (synopsis "R bowtie wrapper")
4899 "This package provides an R wrapper around the popular bowtie short read
4900 aligner and around SpliceMap, a de novo splice junction discovery and
4902 (license license:artistic2.0)))
4904 (define-public r-sgseq
4911 (uri (bioconductor-uri "SGSeq" version))
4914 "0950iv08wd0kjaw55rjn7m6syklvrabwr2zqq74wzyc5afyk2mrw"))))
4915 (properties `((upstream-name . "SGSeq")))
4916 (build-system r-build-system)
4918 `(("r-annotationdbi" ,r-annotationdbi)
4919 ("r-biocgenerics" ,r-biocgenerics)
4920 ("r-biostrings" ,r-biostrings)
4921 ("r-genomeinfodb" ,r-genomeinfodb)
4922 ("r-genomicalignments" ,r-genomicalignments)
4923 ("r-genomicfeatures" ,r-genomicfeatures)
4924 ("r-genomicranges" ,r-genomicranges)
4925 ("r-igraph" ,r-igraph)
4926 ("r-iranges" ,r-iranges)
4927 ("r-rsamtools" ,r-rsamtools)
4928 ("r-rtracklayer" ,r-rtracklayer)
4929 ("r-runit" ,r-runit)
4930 ("r-s4vectors" ,r-s4vectors)
4931 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4932 (home-page "https://bioconductor.org/packages/SGSeq/")
4933 (synopsis "Splice event prediction and quantification from RNA-seq data")
4935 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
4936 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
4937 represented as a splice graph, which can be obtained from existing annotation
4938 or predicted from the mapped sequence reads. Splice events are identified
4939 from the graph and are quantified locally using structurally compatible reads
4940 at the start or end of each splice variant. The software includes functions
4941 for splice event prediction, quantification, visualization and
4943 (license license:artistic2.0)))
4945 (define-public r-rhisat2
4952 (uri (bioconductor-uri "Rhisat2" version))
4955 "02fn5cm8sj2s9x00505y3iyipn1r3lpvpwpjy2pdxdbpmhb5hy49"))))
4956 (properties `((upstream-name . "Rhisat2")))
4957 (build-system r-build-system)
4960 (modify-phases %standard-phases
4961 (add-after 'unpack 'make-reproducible
4963 (substitute* "src/Makefile"
4964 (("`hostname`") "guix")
4966 ;; Avoid shelling out to "which".
4967 (("^CC =.*") (which "gcc"))
4968 (("^CPP =.*") (which "g++")))
4971 `(("r-genomicfeatures" ,r-genomicfeatures)
4972 ("r-genomicranges" ,r-genomicranges)
4973 ("r-sgseq" ,r-sgseq)))
4974 (home-page "https://github.com/fmicompbio/Rhisat2")
4975 (synopsis "R Wrapper for HISAT2 sequence aligner")
4977 "This package provides an R interface to the HISAT2 spliced short-read
4978 aligner by Kim et al. (2015). The package contains wrapper functions to
4979 create a genome index and to perform the read alignment to the generated
4981 (license license:gpl3)))
4983 (define-public r-quasr
4990 (uri (bioconductor-uri "QuasR" version))
4993 "07m5q7wasapj2984kwy897510flbhvz7x0fgs7q2vm5wjhfzdrgv"))))
4994 (properties `((upstream-name . "QuasR")))
4995 (build-system r-build-system)
4999 `(("r-annotationdbi" ,r-annotationdbi)
5000 ("r-biobase" ,r-biobase)
5001 ("r-biocgenerics" ,r-biocgenerics)
5002 ("r-biocmanager" ,r-biocmanager)
5003 ("r-biocparallel" ,r-biocparallel)
5004 ("r-biostrings" ,r-biostrings)
5005 ("r-bsgenome" ,r-bsgenome)
5006 ("r-genomeinfodb" ,r-genomeinfodb)
5007 ("r-genomicalignments" ,r-genomicalignments)
5008 ("r-genomicfeatures" ,r-genomicfeatures)
5009 ("r-genomicfiles" ,r-genomicfiles)
5010 ("r-genomicranges" ,r-genomicranges)
5011 ("r-iranges" ,r-iranges)
5012 ("r-rbowtie" ,r-rbowtie)
5013 ("r-rhisat2" ,r-rhisat2)
5014 ("r-rhtslib" ,r-rhtslib)
5015 ("r-rsamtools" ,r-rsamtools)
5016 ("r-rtracklayer" ,r-rtracklayer)
5017 ("r-s4vectors" ,r-s4vectors)
5018 ("r-shortread" ,r-shortread)))
5019 (home-page "https://bioconductor.org/packages/QuasR/")
5020 (synopsis "Quantify and annotate short reads in R")
5022 "This package provides a framework for the quantification and analysis of
5023 short genomic reads. It covers a complete workflow starting from raw sequence
5024 reads, over creation of alignments and quality control plots, to the
5025 quantification of genomic regions of interest.")
5026 (license license:gpl2)))
5028 (define-public r-rqc
5035 (uri (bioconductor-uri "Rqc" version))
5038 "1nxkrb9kx41g050yz935yrl9pjkakhr8v6whxcvr72gg4r9m2x3m"))))
5039 (properties `((upstream-name . "Rqc")))
5040 (build-system r-build-system)
5042 `(("r-biocgenerics" ,r-biocgenerics)
5043 ("r-biocparallel" ,r-biocparallel)
5044 ("r-biocstyle" ,r-biocstyle)
5045 ("r-biostrings" ,r-biostrings)
5046 ("r-biovizbase" ,r-biovizbase)
5047 ("r-genomicalignments" ,r-genomicalignments)
5048 ("r-genomicfiles" ,r-genomicfiles)
5049 ("r-ggplot2" ,r-ggplot2)
5050 ("r-iranges" ,r-iranges)
5051 ("r-knitr" ,r-knitr)
5052 ("r-markdown" ,r-markdown)
5055 ("r-reshape2" ,r-reshape2)
5056 ("r-rsamtools" ,r-rsamtools)
5057 ("r-s4vectors" ,r-s4vectors)
5058 ("r-shiny" ,r-shiny)
5059 ("r-shortread" ,r-shortread)))
5060 (home-page "https://github.com/labbcb/Rqc")
5061 (synopsis "Quality control tool for high-throughput sequencing data")
5063 "Rqc is an optimized tool designed for quality control and assessment of
5064 high-throughput sequencing data. It performs parallel processing of entire
5065 files and produces a report which contains a set of high-resolution
5067 (license license:gpl2+)))
5069 (define-public r-birewire
5076 (uri (bioconductor-uri "BiRewire" version))
5079 "1074cp422ail72yajn8p0bg26h6zzz07nzypnwfyv86qrpvpdw9q"))))
5080 (properties `((upstream-name . "BiRewire")))
5081 (build-system r-build-system)
5083 `(("r-igraph" ,r-igraph)
5084 ("r-matrix" ,r-matrix)
5086 ("r-tsne" ,r-tsne)))
5087 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5088 (synopsis "Tools for randomization of bipartite graphs")
5090 "This package provides functions for bipartite network rewiring through N
5091 consecutive switching steps and for the computation of the minimal number of
5092 switching steps to be performed in order to maximise the dissimilarity with
5093 respect to the original network. It includes functions for the analysis of
5094 the introduced randomness across the switching steps and several other
5095 routines to analyse the resulting networks and their natural projections.")
5096 (license license:gpl3)))
5098 (define-public r-birta
5105 (uri (bioconductor-uri "birta" version))
5108 "1zhlwapdgkz0fpv5bqfxh9aw6ymnmxnnm1r0n0kfzn5izyjavslg"))))
5109 (build-system r-build-system)
5111 `(("r-biobase" ,r-biobase)
5112 ("r-limma" ,r-limma)
5113 ("r-mass" ,r-mass)))
5114 (home-page "https://bioconductor.org/packages/birta")
5115 (synopsis "Bayesian inference of regulation of transcriptional activity")
5117 "Expression levels of mRNA molecules are regulated by different
5118 processes, comprising inhibition or activation by transcription factors and
5119 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5120 Inference of Regulation of Transcriptional Activity) uses the regulatory
5121 networks of transcription factors and miRNAs together with mRNA and miRNA
5122 expression data to predict switches in regulatory activity between two
5123 conditions. A Bayesian network is used to model the regulatory structure and
5124 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5125 (license license:gpl2+)))
5127 (define-public r-multidataset
5129 (name "r-multidataset")
5134 (uri (bioconductor-uri "MultiDataSet" version))
5137 "0iw99ymrv3ls023mpmgyagmb5simgsgadpj0k4bnssfaqnklywlj"))))
5138 (properties `((upstream-name . "MultiDataSet")))
5139 (build-system r-build-system)
5141 `(("r-biobase" ,r-biobase)
5142 ("r-biocgenerics" ,r-biocgenerics)
5143 ("r-genomicranges" ,r-genomicranges)
5144 ("r-ggplot2" ,r-ggplot2)
5145 ("r-ggrepel" ,r-ggrepel)
5146 ("r-iranges" ,r-iranges)
5147 ("r-limma" ,r-limma)
5148 ("r-qqman" ,r-qqman)
5149 ("r-s4vectors" ,r-s4vectors)
5150 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5151 (home-page "https://bioconductor.org/packages/MultiDataSet/")
5152 (synopsis "Implementation of MultiDataSet and ResultSet")
5154 "This package provides an implementation of the BRGE's (Bioinformatic
5155 Research Group in Epidemiology from Center for Research in Environmental
5156 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
5157 integrating multi omics data sets and ResultSet is a container for omics
5158 results. This package contains base classes for MEAL and rexposome
5160 (license license:expat)))
5162 (define-public r-ropls
5169 (uri (bioconductor-uri "ropls" version))
5172 "05w1zrq92w3jfwq5sdyj27m5qjg4zv7acywia8vd6y5fbgcnyzlp"))))
5173 (build-system r-build-system)
5175 `(("r-biobase" ,r-biobase)
5176 ("r-multidataset" ,r-multidataset)))
5178 `(("r-knitr" ,r-knitr))) ; for vignettes
5179 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5180 (synopsis "Multivariate analysis and feature selection of omics data")
5182 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5183 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5184 regression, classification, and feature selection of omics data where the
5185 number of variables exceeds the number of samples and with multicollinearity
5186 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5187 separately model the variation correlated (predictive) to the factor of
5188 interest and the uncorrelated (orthogonal) variation. While performing
5189 similarly to PLS, OPLS facilitates interpretation.
5191 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5192 analysis and feature selection of omics data. In addition to scores, loadings
5193 and weights plots, the package provides metrics and graphics to determine the
5194 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5195 validity of the model by permutation testing, detect outliers, and perform
5196 feature selection (e.g. with Variable Importance in Projection or regression
5198 (license license:cecill)))
5200 (define-public r-biosigner
5202 (name "r-biosigner")
5207 (uri (bioconductor-uri "biosigner" version))
5210 "1kdfhw629qczrfms0jmphqz0ksjzi8js00xj92h1lnv092npfk0j"))))
5211 (build-system r-build-system)
5213 `(("r-biobase" ,r-biobase)
5214 ("r-e1071" ,r-e1071)
5215 ("r-multidataset" ,r-multidataset)
5216 ("r-randomforest" ,r-randomforest)
5217 ("r-ropls" ,r-ropls)))
5219 `(("r-knitr" ,r-knitr)
5220 ("r-rmarkdown" ,r-rmarkdown)
5221 ("pandoc" ,ghc-pandoc)
5222 ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
5223 (home-page "https://bioconductor.org/packages/biosigner/")
5224 (synopsis "Signature discovery from omics data")
5226 "Feature selection is critical in omics data analysis to extract
5227 restricted and meaningful molecular signatures from complex and high-dimension
5228 data, and to build robust classifiers. This package implements a method to
5229 assess the relevance of the variables for the prediction performances of the
5230 classifier. The approach can be run in parallel with the PLS-DA, Random
5231 Forest, and SVM binary classifiers. The signatures and the corresponding
5232 'restricted' models are returned, enabling future predictions on new
5234 (license license:cecill)))
5236 (define-public r-annotatr
5243 (uri (bioconductor-uri "annotatr" version))
5246 "1bibk3p1q4cavqy11xs6rqqhqdjsq2dd7lf7blwcr27s5ajcd6dj"))))
5247 (build-system r-build-system)
5249 `(("r-annotationdbi" ,r-annotationdbi)
5250 ("r-annotationhub" ,r-annotationhub)
5251 ("r-dplyr" ,r-dplyr)
5252 ("r-genomeinfodb" ,r-genomeinfodb)
5253 ("r-genomicfeatures" ,r-genomicfeatures)
5254 ("r-genomicranges" ,r-genomicranges)
5255 ("r-ggplot2" ,r-ggplot2)
5256 ("r-iranges" ,r-iranges)
5257 ("r-readr" ,r-readr)
5258 ("r-regioner" ,r-regioner)
5259 ("r-reshape2" ,r-reshape2)
5260 ("r-rtracklayer" ,r-rtracklayer)
5261 ("r-s4vectors" ,r-s4vectors)))
5262 (home-page "https://bioconductor.org/packages/annotatr/")
5263 (synopsis "Annotation of genomic regions to genomic annotations")
5265 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5266 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5267 to investigate the intersecting genomic annotations. Such annotations include
5268 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5269 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5270 enhancers. The annotatr package provides an easy way to summarize and
5271 visualize the intersection of genomic sites/regions with genomic
5273 (license license:gpl3)))
5275 (define-public r-rsubread
5282 (uri (bioconductor-uri "Rsubread" version))
5285 "0l8q9y2a4m1di0w5nlxhq9jgliinhgr2fwjpm5ixnqx5j3iprlwd"))))
5286 (properties `((upstream-name . "Rsubread")))
5287 (build-system r-build-system)
5288 (inputs `(("zlib" ,zlib)))
5289 (home-page "https://bioconductor.org/packages/Rsubread/")
5290 (synopsis "Subread sequence alignment and counting for R")
5292 "This package provides tools for alignment, quantification and analysis
5293 of second and third generation sequencing data. It includes functionality for
5294 read mapping, read counting, SNP calling, structural variant detection and
5295 gene fusion discovery. It can be applied to all major sequencing techologies
5296 and to both short and long sequence reads.")
5297 (license license:gpl3)))
5299 (define-public r-flowutils
5301 (name "r-flowutils")
5306 (uri (bioconductor-uri "flowUtils" version))
5309 "1xcs19j9p3izvksyy5wzsbicwby0dsa9g2w7gjzwynzgj5dpfr81"))))
5310 (properties `((upstream-name . "flowUtils")))
5311 (build-system r-build-system)
5313 `(("r-biobase" ,r-biobase)
5314 ("r-corpcor" ,r-corpcor)
5315 ("r-flowcore" ,r-flowcore)
5316 ("r-graph" ,r-graph)
5317 ("r-runit" ,r-runit)
5319 (home-page "https://github.com/jspidlen/flowUtils")
5320 (synopsis "Utilities for flow cytometry")
5322 "This package provides utilities for flow cytometry data.")
5323 (license license:artistic2.0)))
5325 (define-public r-consensusclusterplus
5327 (name "r-consensusclusterplus")
5332 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5335 "0pnh5zy6d3c364xxjdn5zp3kf5afhsxv6yzkdn1qspny0pmqlrp4"))))
5337 `((upstream-name . "ConsensusClusterPlus")))
5338 (build-system r-build-system)
5341 ("r-biobase" ,r-biobase)
5342 ("r-cluster" ,r-cluster)))
5343 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5344 (synopsis "Clustering algorithm")
5346 "This package provides an implementation of an algorithm for determining
5347 cluster count and membership by stability evidence in unsupervised analysis.")
5348 (license license:gpl2)))
5350 (define-public r-cytolib
5357 (uri (bioconductor-uri "cytolib" version))
5360 "1zk5i09k782lw6297gl3rh0g4fxswr2ang8dgqj7p0814l7h15k9"))))
5361 (properties `((upstream-name . "cytolib")))
5362 (build-system r-build-system)
5363 (home-page "https://bioconductor.org/packages/cytolib/")
5364 (synopsis "C++ infrastructure for working with gated cytometry")
5366 "This package provides the core data structure and API to represent and
5367 interact with gated cytometry data.")
5368 (license license:artistic2.0)))
5370 (define-public r-flowcore
5377 (uri (bioconductor-uri "flowCore" version))
5380 "08kvxc187iwlixibx1860jcp5g9bsw8abkv06x2qv1w83fas4pp2"))))
5381 (properties `((upstream-name . "flowCore")))
5382 (build-system r-build-system)
5385 ("r-biobase" ,r-biobase)
5386 ("r-biocgenerics" ,r-biocgenerics)
5387 ("r-cytolib" ,r-cytolib)
5388 ("r-matrixstats" ,r-matrixstats)
5389 ("r-rcpp" ,r-rcpp)))
5390 (home-page "https://bioconductor.org/packages/flowCore")
5391 (synopsis "Basic structures for flow cytometry data")
5393 "This package provides S4 data structures and basic functions to deal
5394 with flow cytometry data.")
5395 (license license:artistic2.0)))
5397 (define-public r-flowmeans
5399 (name "r-flowmeans")
5404 (uri (bioconductor-uri "flowMeans" version))
5407 "1yisrikaafmpb4sig2c5l0wcz4idrs4as7i9x90v6z2v94iq0m8h"))))
5408 (properties `((upstream-name . "flowMeans")))
5409 (build-system r-build-system)
5411 `(("r-biobase" ,r-biobase)
5412 ("r-feature" ,r-feature)
5413 ("r-flowcore" ,r-flowcore)
5414 ("r-rrcov" ,r-rrcov)))
5415 (home-page "https://bioconductor.org/packages/flowMeans")
5416 (synopsis "Non-parametric flow cytometry data gating")
5418 "This package provides tools to identify cell populations in Flow
5419 Cytometry data using non-parametric clustering and segmented-regression-based
5420 change point detection.")
5421 (license license:artistic2.0)))
5423 (define-public r-ncdfflow
5430 (uri (bioconductor-uri "ncdfFlow" version))
5433 "06lscx6h4rg80ifi90rj7z2497b8w1fjipm3l8s3230rkizhh02i"))))
5434 (properties `((upstream-name . "ncdfFlow")))
5435 (build-system r-build-system)
5440 ("r-biobase" ,r-biobase)
5441 ("r-biocgenerics" ,r-biocgenerics)
5442 ("r-flowcore" ,r-flowcore)
5444 ("r-rcpparmadillo" ,r-rcpparmadillo)
5445 ("r-rhdf5lib" ,r-rhdf5lib)
5446 ("r-zlibbioc" ,r-zlibbioc)))
5447 (home-page "https://bioconductor.org/packages/ncdfFlow/")
5448 (synopsis "HDF5 based storage for flow cytometry data")
5450 "This package provides HDF5 storage based methods and functions for
5451 manipulation of flow cytometry data.")
5452 (license license:artistic2.0)))
5454 (define-public r-ggcyto
5461 (uri (bioconductor-uri "ggcyto" version))
5464 "165qszvy5z176h1l3dnjb5dcm279b6bjl5n5gzz8wfn4xpn8anc8"))))
5465 (properties `((upstream-name . "ggcyto")))
5466 (build-system r-build-system)
5468 `(("r-data-table" ,r-data-table)
5469 ("r-flowcore" ,r-flowcore)
5470 ("r-flowworkspace" ,r-flowworkspace)
5471 ("r-ggplot2" ,r-ggplot2)
5472 ("r-gridextra" ,r-gridextra)
5473 ("r-ncdfflow" ,r-ncdfflow)
5475 ("r-rcolorbrewer" ,r-rcolorbrewer)
5476 ("r-rlang" ,r-rlang)
5477 ("r-scales" ,r-scales)))
5478 (home-page "https://github.com/RGLab/ggcyto/issues")
5479 (synopsis "Visualize Cytometry data with ggplot")
5481 "With the dedicated fortify method implemented for @code{flowSet},
5482 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
5483 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
5484 and some custom layers also make it easy to add gates and population
5485 statistics to the plot.")
5486 (license license:artistic2.0)))
5488 (define-public r-flowviz
5495 (uri (bioconductor-uri "flowViz" version))
5498 "0ik16bxcfcg3q26ra3055718kskid64aaazcbqsxalca9ppdm4k7"))))
5499 (properties `((upstream-name . "flowViz")))
5500 (build-system r-build-system)
5502 `(("r-biobase" ,r-biobase)
5503 ("r-flowcore" ,r-flowcore)
5504 ("r-hexbin" ,r-hexbin)
5505 ("r-idpmisc" ,r-idpmisc)
5506 ("r-kernsmooth" ,r-kernsmooth)
5507 ("r-lattice" ,r-lattice)
5508 ("r-latticeextra" ,r-latticeextra)
5510 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5511 (home-page "https://bioconductor.org/packages/flowViz/")
5512 (synopsis "Visualization for flow cytometry")
5514 "This package provides visualization tools for flow cytometry data.")
5515 (license license:artistic2.0)))
5517 (define-public r-flowclust
5519 (name "r-flowclust")
5524 (uri (bioconductor-uri "flowClust" version))
5527 "0k4bgc4mf512njfdfg5ld9l7slgfxyfh766jab87j96zrrgcnj8s"))))
5528 (properties `((upstream-name . "flowClust")))
5529 (build-system r-build-system)
5532 (list "--configure-args=--enable-bundled-gsl=no")))
5534 `(("r-biobase" ,r-biobase)
5535 ("r-biocgenerics" ,r-biocgenerics)
5537 ("r-corpcor" ,r-corpcor)
5538 ("r-ellipse" ,r-ellipse)
5539 ("r-flowcore" ,r-flowcore)
5540 ("r-flowviz" ,r-flowviz)
5541 ("r-graph" ,r-graph)
5542 ("r-mnormt" ,r-mnormt)))
5546 `(("pkg-config" ,pkg-config)))
5547 (home-page "https://bioconductor.org/packages/flowClust")
5548 (synopsis "Clustering for flow cytometry")
5550 "This package provides robust model-based clustering using a t-mixture
5551 model with Box-Cox transformation.")
5552 (license license:artistic2.0)))
5554 ;; TODO: this package bundles an old version of protobuf. It's not easy to
5555 ;; make it use our protobuf package instead.
5556 (define-public r-rprotobuflib
5558 (name "r-rprotobuflib")
5563 (uri (bioconductor-uri "RProtoBufLib" version))
5566 "0dlgki21a37bxqh3cf83vl5zqxm86472g8a9plvhrjzzsn3mwnrm"))))
5567 (properties `((upstream-name . "RProtoBufLib")))
5568 (build-system r-build-system)
5571 (modify-phases %standard-phases
5572 (add-after 'unpack 'unpack-bundled-sources
5574 (with-directory-excursion "src"
5575 (invoke "tar" "xf" "protobuf-2.6.0.tgz"))
5577 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
5578 (synopsis "C++ headers and static libraries of Protocol buffers")
5580 "This package provides the headers and static library of Protocol buffers
5581 for other R packages to compile and link against.")
5582 (license license:bsd-3)))
5584 (define-public r-flowworkspace
5586 (name "r-flowworkspace")
5591 (uri (bioconductor-uri "flowWorkspace" version))
5594 "0hvbkxyylsygra31l1lxyvbsr5hc50lqy1y7gwrfgrfil4a2m762"))))
5595 (properties `((upstream-name . "flowWorkspace")))
5596 (build-system r-build-system)
5599 ("r-biobase" ,r-biobase)
5600 ("r-biocgenerics" ,r-biocgenerics)
5601 ("r-cytolib" ,r-cytolib)
5602 ("r-data-table" ,r-data-table)
5603 ("r-digest" ,r-digest)
5604 ("r-dplyr" ,r-dplyr)
5605 ("r-flowcore" ,r-flowcore)
5606 ("r-flowviz" ,r-flowviz)
5607 ("r-graph" ,r-graph)
5608 ("r-gridextra" ,r-gridextra)
5609 ("r-lattice" ,r-lattice)
5610 ("r-latticeextra" ,r-latticeextra)
5611 ("r-matrixstats" ,r-matrixstats)
5612 ("r-ncdfflow" ,r-ncdfflow)
5614 ("r-rcolorbrewer" ,r-rcolorbrewer)
5616 ("r-rcppparallel" ,r-rcppparallel)
5617 ("r-rgraphviz" ,r-rgraphviz)
5618 ("r-rprotobuflib" ,r-rprotobuflib)
5619 ("r-scales" ,r-scales)
5620 ("r-stringr" ,r-stringr)))
5621 (home-page "https://bioconductor.org/packages/flowWorkspace/")
5622 (synopsis "Infrastructure for working with cytometry data")
5624 "This package is designed to facilitate comparison of automated gating
5625 methods against manual gating done in flowJo. This package allows you to
5626 import basic flowJo workspaces into BioConductor and replicate the gating from
5627 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
5628 samples, compensation, and transformation are performed so that the output
5629 matches the flowJo analysis.")
5630 (license license:artistic2.0)))
5632 (define-public r-flowstats
5634 (name "r-flowstats")
5639 (uri (bioconductor-uri "flowStats" version))
5642 "0pql0lpf90nra7w6z6nd8l9cgjlsg2pxysfravnbzfhl3pjvd96w"))))
5643 (properties `((upstream-name . "flowStats")))
5644 (build-system r-build-system)
5646 `(("r-biobase" ,r-biobase)
5647 ("r-biocgenerics" ,r-biocgenerics)
5648 ("r-cluster" ,r-cluster)
5650 ("r-flowcore" ,r-flowcore)
5651 ("r-flowviz" ,r-flowviz)
5652 ("r-flowworkspace" ,r-flowworkspace)
5653 ("r-kernsmooth" ,r-kernsmooth)
5655 ("r-lattice" ,r-lattice)
5657 ("r-ncdfflow" ,r-ncdfflow)
5658 ("r-rcolorbrewer" ,r-rcolorbrewer)
5659 ("r-rrcov" ,r-rrcov)))
5660 (home-page "http://www.github.com/RGLab/flowStats")
5661 (synopsis "Statistical methods for the analysis of flow cytometry data")
5663 "This package provides methods and functionality to analyze flow data
5664 that is beyond the basic infrastructure provided by the @code{flowCore}
5666 (license license:artistic2.0)))
5668 (define-public r-opencyto
5675 (uri (bioconductor-uri "openCyto" version))
5678 "0h25nhvq1zq624wsgb55wjcgri9rcd2fnqkb31h9jdakr01dw2sb"))))
5679 (properties `((upstream-name . "openCyto")))
5680 (build-system r-build-system)
5682 `(("r-biobase" ,r-biobase)
5683 ("r-biocgenerics" ,r-biocgenerics)
5685 ("r-data-table" ,r-data-table)
5686 ("r-flowclust" ,r-flowclust)
5687 ("r-flowcore" ,r-flowcore)
5688 ("r-flowstats" ,r-flowstats)
5689 ("r-flowviz" ,r-flowviz)
5690 ("r-flowworkspace" ,r-flowworkspace)
5691 ("r-graph" ,r-graph)
5692 ("r-gtools" ,r-gtools)
5694 ("r-lattice" ,r-lattice)
5696 ("r-ncdfflow" ,r-ncdfflow)
5698 ("r-r-utils" ,r-r-utils)
5700 ("r-rcolorbrewer" ,r-rcolorbrewer)
5702 ("r-rrcov" ,r-rrcov)))
5703 (home-page "https://bioconductor.org/packages/openCyto")
5704 (synopsis "Hierarchical gating pipeline for flow cytometry data")
5706 "This package is designed to facilitate the automated gating methods in a
5707 sequential way to mimic the manual gating strategy.")
5708 (license license:artistic2.0)))
5710 (define-public r-cytoml
5717 (uri (bioconductor-uri "CytoML" version))
5720 "0m8x18wkvis85cawv7j07pk59w76wnzy93ia99gd24j82z4h97p1"))))
5721 (properties `((upstream-name . "CytoML")))
5722 (build-system r-build-system)
5724 `(("libxml2" ,libxml2)))
5726 `(("r-base64enc" ,r-base64enc)
5728 ("r-biobase" ,r-biobase)
5729 ("r-corpcor" ,r-corpcor)
5730 ("r-cytolib" ,r-cytolib)
5731 ("r-data-table" ,r-data-table)
5732 ("r-dplyr" ,r-dplyr)
5733 ("r-flowcore" ,r-flowcore)
5734 ("r-flowworkspace" ,r-flowworkspace)
5735 ("r-ggcyto" ,r-ggcyto)
5736 ("r-graph" ,r-graph)
5737 ("r-jsonlite" ,r-jsonlite)
5738 ("r-lattice" ,r-lattice)
5739 ("r-ncdfflow" ,r-ncdfflow)
5740 ("r-opencyto" ,r-opencyto)
5744 ("r-rcppparallel" ,r-rcppparallel)
5745 ("r-rgraphviz" ,r-rgraphviz)
5746 ("r-rprotobuflib" ,r-rprotobuflib)
5747 ("r-runit" ,r-runit)
5749 ("r-yaml" ,r-yaml)))
5750 (home-page "https://github.com/RGLab/CytoML")
5751 (synopsis "GatingML interface for cross platform cytometry data sharing")
5753 "This package provides an interface to implementations of the GatingML2.0
5754 standard to exchange gated cytometry data with other software platforms.")
5755 (license license:artistic2.0)))
5757 (define-public r-flowsom
5764 (uri (bioconductor-uri "FlowSOM" version))
5767 "0265sq4zvj6d6h5ghqj9xzm4b0z9v65kgyl88cgdcpdkzfnfcvd5"))))
5768 (properties `((upstream-name . "FlowSOM")))
5769 (build-system r-build-system)
5771 `(("r-biocgenerics" ,r-biocgenerics)
5772 ("r-consensusclusterplus" ,r-consensusclusterplus)
5773 ("r-cytoml" ,r-cytoml)
5774 ("r-flowcore" ,r-flowcore)
5775 ("r-flowworkspace" ,r-flowworkspace)
5776 ("r-igraph" ,r-igraph)
5777 ("r-rcolorbrewer" ,r-rcolorbrewer)
5780 (home-page "https://bioconductor.org/packages/FlowSOM/")
5781 (synopsis "Visualize and interpret cytometry data")
5783 "FlowSOM offers visualization options for cytometry data, by using
5784 self-organizing map clustering and minimal spanning trees.")
5785 (license license:gpl2+)))
5787 (define-public r-mixomics
5794 (uri (bioconductor-uri "mixOmics" version))
5797 "18jwrdyc4pnx917y1kskxz3fqvlrkyy4ny0xqrfcidz0j7p0b7wr"))))
5798 (properties `((upstream-name . "mixOmics")))
5799 (build-system r-build-system)
5801 `(("r-corpcor" ,r-corpcor)
5802 ("r-dplyr" ,r-dplyr)
5803 ("r-ellipse" ,r-ellipse)
5804 ("r-ggplot2" ,r-ggplot2)
5805 ("r-gridextra" ,r-gridextra)
5806 ("r-igraph" ,r-igraph)
5807 ("r-lattice" ,r-lattice)
5809 ("r-matrixstats" ,r-matrixstats)
5810 ("r-rarpack" ,r-rarpack)
5811 ("r-rcolorbrewer" ,r-rcolorbrewer)
5812 ("r-reshape2" ,r-reshape2)
5813 ("r-tidyr" ,r-tidyr)))
5814 (home-page "http://www.mixOmics.org")
5815 (synopsis "Multivariate methods for exploration of biological datasets")
5817 "mixOmics offers a wide range of multivariate methods for the exploration
5818 and integration of biological datasets with a particular focus on variable
5819 selection. The package proposes several sparse multivariate models we have
5820 developed to identify the key variables that are highly correlated, and/or
5821 explain the biological outcome of interest. The data that can be analysed
5822 with mixOmics may come from high throughput sequencing technologies, such as
5823 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
5824 also beyond the realm of omics (e.g. spectral imaging). The methods
5825 implemented in mixOmics can also handle missing values without having to
5826 delete entire rows with missing data.")
5827 (license license:gpl2+)))
5829 (define-public r-depecher
5836 (uri (bioconductor-uri "DepecheR" version))
5839 "1f6zbc0fq7xjflh3mkjx1n83mpppw663dj22rlpxzwp1kpmf6wm5"))))
5840 (properties `((upstream-name . "DepecheR")))
5841 (build-system r-build-system)
5843 `(("r-beanplot" ,r-beanplot)
5844 ("r-dosnow" ,r-dosnow)
5845 ("r-dplyr" ,r-dplyr)
5847 ("r-foreach" ,r-foreach)
5848 ("r-ggplot2" ,r-ggplot2)
5849 ("r-gplots" ,r-gplots)
5851 ("r-matrixstats" ,r-matrixstats)
5852 ("r-mixomics" ,r-mixomics)
5853 ("r-moments" ,r-moments)
5855 ("r-rcppeigen" ,r-rcppeigen)
5856 ("r-reshape2" ,r-reshape2)
5857 ("r-robustbase" ,r-robustbase)
5858 ("r-viridis" ,r-viridis)))
5859 (home-page "https://bioconductor.org/packages/DepecheR/")
5860 (synopsis "Identify traits of clusters in high-dimensional entities")
5862 "The purpose of this package is to identify traits in a dataset that can
5863 separate groups. This is done on two levels. First, clustering is performed,
5864 using an implementation of sparse K-means. Secondly, the generated clusters
5865 are used to predict outcomes of groups of individuals based on their
5866 distribution of observations in the different clusters. As certain clusters
5867 with separating information will be identified, and these clusters are defined
5868 by a sparse number of variables, this method can reduce the complexity of
5869 data, to only emphasize the data that actually matters.")
5870 (license license:expat)))
5872 (define-public r-rcistarget
5874 (name "r-rcistarget")
5879 (uri (bioconductor-uri "RcisTarget" version))
5882 "1nnah7s0jd24fpfyxsf76jas8dm23c3266aps124wdlqsp9q5qjw"))))
5883 (properties `((upstream-name . "RcisTarget")))
5884 (build-system r-build-system)
5886 `(("r-aucell" ,r-aucell)
5887 ("r-biocgenerics" ,r-biocgenerics)
5888 ("r-data-table" ,r-data-table)
5889 ("r-feather" ,r-feather)
5890 ("r-gseabase" ,r-gseabase)
5891 ("r-r-utils" ,r-r-utils)
5892 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5893 (home-page "https://aertslab.org/#scenic")
5894 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
5896 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
5897 over-represented on a gene list. In a first step, RcisTarget selects DNA
5898 motifs that are significantly over-represented in the surroundings of the
5899 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
5900 achieved by using a database that contains genome-wide cross-species rankings
5901 for each motif. The motifs that are then annotated to TFs and those that have
5902 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
5903 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
5904 genes in the gene-set that are ranked above the leading edge).")
5905 (license license:gpl3)))
5907 (define-public r-cicero
5914 (uri (bioconductor-uri "cicero" version))
5917 "0mmm7vvzq50b5fayid0bw82b5lar3xm9fwl2ya30q0p4db2y6wnz"))))
5918 (build-system r-build-system)
5920 `(("r-assertthat" ,r-assertthat)
5921 ("r-biobase" ,r-biobase)
5922 ("r-biocgenerics" ,r-biocgenerics)
5923 ("r-data-table" ,r-data-table)
5924 ("r-dplyr" ,r-dplyr)
5926 ("r-genomicranges" ,r-genomicranges)
5927 ("r-ggplot2" ,r-ggplot2)
5928 ("r-glasso" ,r-glasso)
5930 ("r-igraph" ,r-igraph)
5931 ("r-iranges" ,r-iranges)
5932 ("r-matrix" ,r-matrix)
5933 ("r-monocle" ,r-monocle)
5935 ("r-reshape2" ,r-reshape2)
5936 ("r-s4vectors" ,r-s4vectors)
5937 ("r-stringr" ,r-stringr)
5938 ("r-tibble" ,r-tibble)
5939 ("r-vgam" ,r-vgam)))
5940 (home-page "https://bioconductor.org/packages/cicero/")
5941 (synopsis "Predict cis-co-accessibility from single-cell data")
5943 "Cicero computes putative cis-regulatory maps from single-cell chromatin
5944 accessibility data. It also extends the monocle package for use in chromatin
5945 accessibility data.")
5946 (license license:expat)))
5948 ;; This is the latest commit on the "monocle3" branch.
5949 (define-public r-cicero-monocle3
5950 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
5952 (package (inherit r-cicero)
5953 (name "r-cicero-monocle3")
5954 (version (git-version "1.3.2" revision commit))
5959 (url "https://github.com/cole-trapnell-lab/cicero-release.git")
5961 (file-name (git-file-name name version))
5964 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
5966 `(("r-monocle3" ,r-monocle3)
5967 ,@(alist-delete "r-monocle"
5968 (package-propagated-inputs r-cicero)))))))
5970 (define-public r-cistopic
5971 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
5975 (version (git-version "0.2.1" revision commit))
5980 (url "https://github.com/aertslab/cisTopic.git")
5982 (file-name (git-file-name name version))
5985 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
5986 (build-system r-build-system)
5988 `(("r-aucell" ,r-aucell)
5989 ("r-data-table" ,r-data-table)
5990 ("r-dplyr" ,r-dplyr)
5991 ("r-dosnow" ,r-dosnow)
5993 ("r-feather" ,r-feather)
5994 ("r-fitdistrplus" ,r-fitdistrplus)
5995 ("r-genomicranges" ,r-genomicranges)
5996 ("r-ggplot2" ,r-ggplot2)
5998 ("r-matrix" ,r-matrix)
6000 ("r-rcistarget" ,r-rcistarget)
6001 ("r-rtracklayer" ,r-rtracklayer)
6002 ("r-s4vectors" ,r-s4vectors)))
6003 (home-page "https://github.com/aertslab/cisTopic")
6004 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
6006 "The sparse nature of single cell epigenomics data can be overruled using
6007 probabilistic modelling methods such as @dfn{Latent Dirichlet
6008 Allocation} (LDA). This package allows the probabilistic modelling of
6009 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
6010 includes functionalities to identify cell states based on the contribution of
6011 cisTopics and explore the nature and regulatory proteins driving them.")
6012 (license license:gpl3))))
6014 (define-public r-genie3
6021 (uri (bioconductor-uri "GENIE3" version))
6024 "0p67lhgy3lb4nc958s51hx7rvgwhzwfic9xhpsrask40k43spv7l"))))
6025 (properties `((upstream-name . "GENIE3")))
6026 (build-system r-build-system)
6027 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
6028 (home-page "https://bioconductor.org/packages/GENIE3")
6029 (synopsis "Gene network inference with ensemble of trees")
6031 "This package implements the GENIE3 algorithm for inferring gene
6032 regulatory networks from expression data.")
6033 (license license:gpl2+)))
6035 (define-public r-roc
6042 (uri (bioconductor-uri "ROC" version))
6045 "1aqpyc28czagg3nbybh55vf152nbar61jjw79w04326d97mc3j3y"))))
6046 (properties `((upstream-name . "ROC")))
6047 (build-system r-build-system)
6049 `(("r-knitr" ,r-knitr)))
6050 (home-page "https://www.bioconductor.org/packages/ROC/")
6051 (synopsis "Utilities for ROC curves")
6053 "This package provides utilities for @dfn{Receiver Operating
6054 Characteristic} (ROC) curves, with a focus on micro arrays.")
6055 (license license:artistic2.0)))
6057 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
6059 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
6064 (uri (bioconductor-uri
6065 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
6066 version 'annotation))
6069 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
6072 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
6073 (build-system r-build-system)
6074 (propagated-inputs `(("r-minfi" ,r-minfi)))
6076 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
6077 (synopsis "Annotation for Illumina's 450k methylation arrays")
6079 "This package provides manifests and annotation for Illumina's 450k array
6081 (license license:artistic2.0)))
6083 (define-public r-watermelon
6085 (name "r-watermelon")
6090 (uri (bioconductor-uri "wateRmelon" version))
6093 "0a66fq04yph9dis91lzjk9kh134zy6fj98yklrwf24r1080qngx0"))))
6094 (properties `((upstream-name . "wateRmelon")))
6095 (build-system r-build-system)
6097 `(("r-biobase" ,r-biobase)
6098 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
6099 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
6100 ("r-illuminaio" ,r-illuminaio)
6101 ("r-limma" ,r-limma)
6103 ("r-matrixstats" ,r-matrixstats)
6104 ("r-methylumi" ,r-methylumi)
6106 (home-page "https://bioconductor.org/packages/wateRmelon/")
6107 (synopsis "Illumina 450 methylation array normalization and metrics")
6109 "The standard index of DNA methylation (beta) is computed from methylated
6110 and unmethylated signal intensities. Betas calculated from raw signal
6111 intensities perform well, but using 11 methylomic datasets we demonstrate that
6112 quantile normalization methods produce marked improvement. The commonly used
6113 procedure of normalizing betas is inferior to the separate normalization of M
6114 and U, and it is also advantageous to normalize Type I and Type II assays
6115 separately. This package provides 15 flavours of betas and three performance
6116 metrics, with methods for objects produced by the @code{methylumi} and
6117 @code{minfi} packages.")
6118 (license license:gpl3)))
6120 (define-public r-gdsfmt
6127 (uri (bioconductor-uri "gdsfmt" version))
6130 "0zc9v62imd0ykz4h30pxa64q0y45qijmkwdk2pd4ncsg8fc2jlz9"))
6131 (modules '((guix build utils)))
6132 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
6133 ;; them and link with system libraries instead.
6136 (for-each delete-file-recursively
6140 (substitute* "src/Makevars"
6141 (("all: \\$\\(SHLIB\\)") "all:")
6142 (("\\$\\(SHLIB\\): liblzma.a") "")
6143 (("(ZLIB|LZ4)/.*") "")
6144 (("CoreArray/dVLIntGDS.cpp.*")
6145 "CoreArray/dVLIntGDS.cpp")
6146 (("CoreArray/dVLIntGDS.o.*")
6147 "CoreArray/dVLIntGDS.o")
6148 (("PKG_LIBS = ./liblzma.a")
6149 "PKG_LIBS = -llz4"))
6150 (substitute* "src/CoreArray/dStream.h"
6151 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
6152 (string-append "include <" header ">")))
6154 (properties `((upstream-name . "gdsfmt")))
6155 (build-system r-build-system)
6160 (home-page "http://corearray.sourceforge.net/")
6162 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
6164 "This package provides a high-level R interface to CoreArray @dfn{Genomic
6165 Data Structure} (GDS) data files, which are portable across platforms with
6166 hierarchical structure to store multiple scalable array-oriented data sets
6167 with metadata information. It is suited for large-scale datasets, especially
6168 for data which are much larger than the available random-access memory. The
6169 @code{gdsfmt} package offers efficient operations specifically designed for
6170 integers of less than 8 bits, since a diploid genotype, like
6171 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
6172 byte. Data compression and decompression are available with relatively
6173 efficient random access. It is also allowed to read a GDS file in parallel
6174 with multiple R processes supported by the package @code{parallel}.")
6175 (license license:lgpl3)))
6177 (define-public r-bigmelon
6184 (uri (bioconductor-uri "bigmelon" version))
6187 "0sw7rp4p03m1s72b4j06jfb7as3v1n2w2z4ppk8s4f80fb05bcls"))))
6188 (properties `((upstream-name . "bigmelon")))
6189 (build-system r-build-system)
6191 `(("r-biobase" ,r-biobase)
6192 ("r-biocgenerics" ,r-biocgenerics)
6193 ("r-gdsfmt" ,r-gdsfmt)
6194 ("r-geoquery" ,r-geoquery)
6195 ("r-methylumi" ,r-methylumi)
6196 ("r-minfi" ,r-minfi)
6197 ("r-watermelon" ,r-watermelon)))
6198 (home-page "https://bioconductor.org/packages/bigmelon/")
6199 (synopsis "Illumina methylation array analysis for large experiments")
6201 "This package provides methods for working with Illumina arrays using the
6202 @code{gdsfmt} package.")
6203 (license license:gpl3)))
6205 (define-public r-seqbias
6212 (uri (bioconductor-uri "seqbias" version))
6215 "19vbdyjblij2533ibmrw1n0rkqfrbflma6cg5b79ghks0mg7z8hq"))))
6216 (properties `((upstream-name . "seqbias")))
6217 (build-system r-build-system)
6219 `(("r-biostrings" ,r-biostrings)
6220 ("r-genomicranges" ,r-genomicranges)
6221 ("r-rhtslib" ,r-rhtslib)))
6223 `(("zlib" ,zlib))) ; This comes from rhtslib.
6224 (home-page "https://bioconductor.org/packages/seqbias/")
6225 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
6227 "This package implements a model of per-position sequencing bias in
6228 high-throughput sequencing data using a simple Bayesian network, the structure
6229 and parameters of which are trained on a set of aligned reads and a reference
6231 (license license:lgpl3)))
6233 (define-public r-reqon
6240 (uri (bioconductor-uri "ReQON" version))
6243 "10p6l2zxijqyypdm970jyfqyrnfhaq3nf7cg2q6mgd1srggfa0cx"))))
6244 (properties `((upstream-name . "ReQON")))
6245 (build-system r-build-system)
6247 `(("r-rjava" ,r-rjava)
6248 ("r-rsamtools" ,r-rsamtools)
6249 ("r-seqbias" ,r-seqbias)))
6250 (home-page "https://bioconductor.org/packages/ReQON/")
6251 (synopsis "Recalibrating quality of nucleotides")
6253 "This package provides an implementation of an algorithm for
6254 recalibrating the base quality scores for aligned sequencing data in BAM
6256 (license license:gpl2)))
6258 (define-public r-wavcluster
6260 (name "r-wavcluster")
6265 (uri (bioconductor-uri "wavClusteR" version))
6268 "0vq3xxsvwq86rlya7xc92sc4i6b48sib0pcina3xivg3ky2j3z7y"))))
6269 (properties `((upstream-name . "wavClusteR")))
6270 (build-system r-build-system)
6272 `(("r-biocgenerics" ,r-biocgenerics)
6273 ("r-biostrings" ,r-biostrings)
6274 ("r-foreach" ,r-foreach)
6275 ("r-genomicfeatures" ,r-genomicfeatures)
6276 ("r-genomicranges" ,r-genomicranges)
6277 ("r-ggplot2" ,r-ggplot2)
6278 ("r-hmisc" ,r-hmisc)
6279 ("r-iranges" ,r-iranges)
6280 ("r-mclust" ,r-mclust)
6281 ("r-rsamtools" ,r-rsamtools)
6282 ("r-rtracklayer" ,r-rtracklayer)
6283 ("r-s4vectors" ,r-s4vectors)
6284 ("r-seqinr" ,r-seqinr)
6285 ("r-stringr" ,r-stringr)
6286 ("r-wmtsa" ,r-wmtsa)))
6287 (home-page "https://bioconductor.org/packages/wavClusteR/")
6288 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
6290 "This package provides an integrated pipeline for the analysis of
6291 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
6292 sequencing errors, SNPs and additional non-experimental sources by a non-
6293 parametric mixture model. The protein binding sites (clusters) are then
6294 resolved at high resolution and cluster statistics are estimated using a
6295 rigorous Bayesian framework. Post-processing of the results, data export for
6296 UCSC genome browser visualization and motif search analysis are provided. In
6297 addition, the package allows to integrate RNA-Seq data to estimate the False
6298 Discovery Rate of cluster detection. Key functions support parallel multicore
6299 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
6300 be applied to the analysis of other NGS data obtained from experimental
6301 procedures that induce nucleotide substitutions (e.g. BisSeq).")
6302 (license license:gpl2)))
6304 (define-public r-timeseriesexperiment
6306 (name "r-timeseriesexperiment")
6311 (uri (bioconductor-uri "TimeSeriesExperiment" version))
6314 "0xqa6hzknnci20zx2f6mw5cpqx8pq0v6fzf053hh51p1l2ikvgqm"))))
6316 `((upstream-name . "TimeSeriesExperiment")))
6317 (build-system r-build-system)
6319 `(("r-deseq2" ,r-deseq2)
6320 ("r-dplyr" ,r-dplyr)
6321 ("r-dynamictreecut" ,r-dynamictreecut)
6322 ("r-edger" ,r-edger)
6323 ("r-ggplot2" ,r-ggplot2)
6324 ("r-hmisc" ,r-hmisc)
6325 ("r-limma" ,r-limma)
6326 ("r-magrittr" ,r-magrittr)
6327 ("r-proxy" ,r-proxy)
6328 ("r-s4vectors" ,r-s4vectors)
6329 ("r-summarizedexperiment" ,r-summarizedexperiment)
6330 ("r-tibble" ,r-tibble)
6331 ("r-tidyr" ,r-tidyr)
6332 ("r-vegan" ,r-vegan)
6333 ("r-viridis" ,r-viridis)))
6334 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
6335 (synopsis "Analysis for short time-series data")
6337 "This package is a visualization and analysis toolbox for short time
6338 course data which includes dimensionality reduction, clustering, two-sample
6339 differential expression testing and gene ranking techniques. The package also
6340 provides methods for retrieving enriched pathways.")
6341 (license license:lgpl3+)))
6343 (define-public r-variantfiltering
6345 (name "r-variantfiltering")
6350 (uri (bioconductor-uri "VariantFiltering" version))
6353 "13pgfk2mbffd9smmxnwz7g0jrwng78711053wfzadr107zbyn4r8"))))
6355 `((upstream-name . "VariantFiltering")))
6356 (build-system r-build-system)
6358 `(("r-annotationdbi" ,r-annotationdbi)
6359 ("r-biobase" ,r-biobase)
6360 ("r-biocgenerics" ,r-biocgenerics)
6361 ("r-biocparallel" ,r-biocparallel)
6362 ("r-biostrings" ,r-biostrings)
6363 ("r-bsgenome" ,r-bsgenome)
6365 ("r-genomeinfodb" ,r-genomeinfodb)
6366 ("r-genomicfeatures" ,r-genomicfeatures)
6367 ("r-genomicranges" ,r-genomicranges)
6368 ("r-genomicscores" ,r-genomicscores)
6369 ("r-graph" ,r-graph)
6371 ("r-iranges" ,r-iranges)
6373 ("r-rsamtools" ,r-rsamtools)
6374 ("r-s4vectors" ,r-s4vectors)
6375 ("r-shiny" ,r-shiny)
6376 ("r-shinyjs" ,r-shinyjs)
6377 ("r-shinythemes" ,r-shinythemes)
6378 ("r-shinytree" ,r-shinytree)
6379 ("r-summarizedexperiment" ,r-summarizedexperiment)
6380 ("r-variantannotation" ,r-variantannotation)
6381 ("r-xvector" ,r-xvector)))
6382 (home-page "https://github.com/rcastelo/VariantFiltering")
6383 (synopsis "Filtering of coding and non-coding genetic variants")
6385 "Filter genetic variants using different criteria such as inheritance
6386 model, amino acid change consequence, minor allele frequencies across human
6387 populations, splice site strength, conservation, etc.")
6388 (license license:artistic2.0)))
6390 (define-public r-genomegraphs
6392 (name "r-genomegraphs")
6397 (uri (bioconductor-uri "GenomeGraphs" version))
6400 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
6401 (properties `((upstream-name . "GenomeGraphs")))
6402 (build-system r-build-system)
6404 `(("r-biomart" ,r-biomart)))
6405 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
6406 (synopsis "Plotting genomic information from Ensembl")
6408 "Genomic data analyses requires integrated visualization of known genomic
6409 information and new experimental data. GenomeGraphs uses the biomaRt package
6410 to perform live annotation queries to Ensembl and translates this to e.g.
6411 gene/transcript structures in viewports of the grid graphics package. This
6412 results in genomic information plotted together with your data. Another
6413 strength of GenomeGraphs is to plot different data types such as array CGH,
6414 gene expression, sequencing and other data, together in one plot using the
6415 same genome coordinate system.")
6416 (license license:artistic2.0)))
6418 (define-public r-wavetiling
6420 (name "r-wavetiling")
6425 (uri (bioconductor-uri "waveTiling" version))
6428 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
6429 (properties `((upstream-name . "waveTiling")))
6430 (build-system r-build-system)
6432 `(("r-affy" ,r-affy)
6433 ("r-biobase" ,r-biobase)
6434 ("r-biostrings" ,r-biostrings)
6435 ("r-genomegraphs" ,r-genomegraphs)
6436 ("r-genomicranges" ,r-genomicranges)
6437 ("r-iranges" ,r-iranges)
6438 ("r-oligo" ,r-oligo)
6439 ("r-oligoclasses" ,r-oligoclasses)
6440 ("r-preprocesscore" ,r-preprocesscore)
6441 ("r-waveslim" ,r-waveslim)))
6442 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
6443 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
6445 "This package is designed to conduct transcriptome analysis for tiling
6446 arrays based on fast wavelet-based functional models.")
6447 (license license:gpl2+)))
6449 (define-public r-variancepartition
6451 (name "r-variancepartition")
6456 (uri (bioconductor-uri "variancePartition" version))
6459 "1ygx7f2sp4b7ilgspm6vqcbjxs7br9s6g3gwcdb978kx03ymp4i8"))))
6461 `((upstream-name . "variancePartition")))
6462 (build-system r-build-system)
6464 `(("r-biobase" ,r-biobase)
6465 ("r-biocparallel" ,r-biocparallel)
6466 ("r-colorramps" ,r-colorramps)
6467 ("r-doparallel" ,r-doparallel)
6468 ("r-foreach" ,r-foreach)
6469 ("r-ggplot2" ,r-ggplot2)
6470 ("r-gplots" ,r-gplots)
6471 ("r-iterators" ,r-iterators)
6472 ("r-limma" ,r-limma)
6474 ("r-lmertest" ,r-lmertest)
6476 ("r-pbkrtest" ,r-pbkrtest)
6477 ("r-progress" ,r-progress)
6478 ("r-reshape2" ,r-reshape2)
6479 ("r-scales" ,r-scales)))
6480 (home-page "https://bioconductor.org/packages/variancePartition/")
6481 (synopsis "Analyze variation in gene expression experiments")
6483 "This is a package providing tools to quantify and interpret multiple
6484 sources of biological and technical variation in gene expression experiments.
6485 It uses a linear mixed model to quantify variation in gene expression
6486 attributable to individual, tissue, time point, or technical variables. The
6487 package includes dream differential expression analysis for repeated
6489 (license license:gpl2+)))
6491 (define-public r-htqpcr
6498 (uri (bioconductor-uri "HTqPCR" version))
6501 "008iczqaa0wn5nw144vfg3qylg7qa1q963nq9mqhgj3sxlg4rmjx"))))
6502 (properties `((upstream-name . "HTqPCR")))
6503 (build-system r-build-system)
6505 `(("r-affy" ,r-affy)
6506 ("r-biobase" ,r-biobase)
6507 ("r-gplots" ,r-gplots)
6508 ("r-limma" ,r-limma)
6509 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6510 (home-page "http://www.ebi.ac.uk/bertone/software")
6511 (synopsis "Automated analysis of high-throughput qPCR data")
6513 "Analysis of Ct values from high throughput quantitative real-time
6514 PCR (qPCR) assays across multiple conditions or replicates. The input data
6515 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
6516 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
6517 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
6518 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
6519 loading, quality assessment, normalization, visualization and parametric or
6520 non-parametric testing for statistical significance in Ct values between
6521 features (e.g. genes, microRNAs).")
6522 (license license:artistic2.0)))
6524 (define-public r-unifiedwmwqpcr
6526 (name "r-unifiedwmwqpcr")
6531 (uri (bioconductor-uri "unifiedWMWqPCR" version))
6534 "1l6rf7scxxyz4x0m4li54y6905sqj4jrx481zb9h3vqhcfcmn8lj"))))
6536 `((upstream-name . "unifiedWMWqPCR")))
6537 (build-system r-build-system)
6539 `(("r-biocgenerics" ,r-biocgenerics)
6540 ("r-htqpcr" ,r-htqpcr)))
6541 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
6542 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
6544 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
6545 data. This modified test allows for testing differential expression in qPCR
6547 (license license:gpl2+)))
6549 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
6551 (define-public r-activedriverwgs
6553 (name "r-activedriverwgs")
6558 (uri (cran-uri "ActiveDriverWGS" version))
6561 "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1"))))
6563 `((upstream-name . "ActiveDriverWGS")))
6564 (build-system r-build-system)
6566 `(("r-biostrings" ,r-biostrings)
6567 ("r-bsgenome" ,r-bsgenome)
6568 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
6569 ("r-genomeinfodb" ,r-genomeinfodb)
6570 ("r-genomicranges" ,r-genomicranges)
6571 ("r-iranges" ,r-iranges)
6573 ("r-s4vectors" ,r-s4vectors)))
6574 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
6575 (synopsis "Driver discovery tool for cancer whole genomes")
6577 "This package provides a method for finding an enrichment of cancer
6578 simple somatic mutations (SNVs and Indels) in functional elements across the
6579 human genome. ActiveDriverWGS detects coding and noncoding driver elements
6580 using whole genome sequencing data.")
6581 (license license:gpl3)))
6583 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
6585 (define-public r-activepathways
6587 (name "r-activepathways")
6592 (uri (cran-uri "ActivePathways" version))
6595 "1xb0d1svmzw404pv8ja6wr4773k7x2lxkrzrayilvzqbfzj1wx20"))))
6597 `((upstream-name . "ActivePathways")))
6598 (build-system r-build-system)
6600 `(("r-data-table" ,r-data-table)
6601 ("r-ggplot2" ,r-ggplot2)
6602 ("r-metap" ,r-metap)))
6603 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
6604 (synopsis "Multivariate pathway enrichment analysis")
6606 "This package represents an integrative method of analyzing multi omics
6607 data that conducts enrichment analysis of annotated gene sets. ActivePathways
6608 uses a statistical data fusion approach, rationalizes contributing evidence
6609 and highlights associated genes, improving systems-level understanding of
6610 cellular organization in health and disease.")
6611 (license license:gpl3)))
6613 (define-public r-bgmix
6620 (uri (bioconductor-uri "BGmix" version))
6623 "1bwqqhkh4m3hhpd71grwjrg7n07lzvys4y7aghmw2gw5ibnk5683"))))
6624 (properties `((upstream-name . "BGmix")))
6625 (build-system r-build-system)
6627 `(("r-kernsmooth" ,r-kernsmooth)))
6628 (home-page "https://bioconductor.org/packages/BGmix/")
6629 (synopsis "Bayesian models for differential gene expression")
6631 "This package provides fully Bayesian mixture models for differential
6633 (license license:gpl2)))
6635 (define-public r-bgx
6642 (uri (bioconductor-uri "bgx" version))
6645 "0fiqqv6pin0zhxaw67hzfjccq2qkl9qfqjf10nx2zmpxm2licavm"))))
6646 (properties `((upstream-name . "bgx")))
6647 (build-system r-build-system)
6649 `(("r-affy" ,r-affy)
6650 ("r-biobase" ,r-biobase)
6651 ("r-gcrma" ,r-gcrma)
6652 ("r-rcpp" ,r-rcpp)))
6653 (home-page "https://bioconductor.org/packages/bgx/")
6654 (synopsis "Bayesian gene expression")
6656 "This package provides tools for Bayesian integrated analysis of
6657 Affymetrix GeneChips.")
6658 (license license:gpl2)))
6660 (define-public r-bhc
6667 (uri (bioconductor-uri "BHC" version))
6670 "1bxx3jak8mgvay3j1xd59bb9j86pzl6hh5abxww9x1b7rswmy1jh"))))
6671 (properties `((upstream-name . "BHC")))
6672 (build-system r-build-system)
6673 (home-page "https://bioconductor.org/packages/BHC/")
6674 (synopsis "Bayesian hierarchical clustering")
6676 "The method implemented in this package performs bottom-up hierarchical
6677 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
6678 in the data and Bayesian model selection to decide at each step which clusters
6679 to merge. This avoids several limitations of traditional methods, for example
6680 how many clusters there should be and how to choose a principled distance
6681 metric. This implementation accepts multinomial (i.e. discrete, with 2+
6682 categories) or time-series data. This version also includes a randomised
6683 algorithm which is more efficient for larger data sets.")
6684 (license license:gpl3)))
6686 (define-public r-bicare
6693 (uri (bioconductor-uri "BicARE" version))
6696 "1gia5vzmvbk4k1vx3bh9nld1ws9s3c0y11qfbzqhfnfjbd7n8qcs"))))
6697 (properties `((upstream-name . "BicARE")))
6698 (build-system r-build-system)
6700 `(("r-biobase" ,r-biobase)
6701 ("r-gseabase" ,r-gseabase)
6702 ("r-multtest" ,r-multtest)))
6703 (home-page "http://bioinfo.curie.fr")
6704 (synopsis "Biclustering analysis and results exploration")
6706 "This is a package for biclustering analysis and exploration of
6708 (license license:gpl2)))
6710 (define-public r-bifet
6717 (uri (bioconductor-uri "BiFET" version))
6720 "0ck1d6hxd4f40hfz8p2z5xmjbz79yhrf6fisjka2xzk5v9fm4p4k"))))
6721 (properties `((upstream-name . "BiFET")))
6722 (build-system r-build-system)
6724 `(("r-genomicranges" ,r-genomicranges)
6725 ("r-poibin" ,r-poibin)))
6726 (home-page "https://bioconductor.org/packages/BiFET")
6727 (synopsis "Bias-free footprint enrichment test")
6729 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
6730 over-represented in target regions compared to background regions after
6731 correcting for the bias arising from the imbalance in read counts and GC
6732 contents between the target and background regions. For a given TF k, BiFET
6733 tests the null hypothesis that the target regions have the same probability of
6734 having footprints for the TF k as the background regions while correcting for
6735 the read count and GC content bias.")
6736 (license license:gpl3)))
6738 (define-public r-rsbml
6745 (uri (bioconductor-uri "rsbml" version))
6748 "1dbp0aaijxn3na26b68ws0v9qzvml61ifb9z4i8pz7q6h48n7lxa"))))
6749 (properties `((upstream-name . "rsbml")))
6750 (build-system r-build-system)
6752 `(("libsbml" ,libsbml)
6755 `(("r-biocgenerics" ,r-biocgenerics)
6756 ("r-graph" ,r-graph)))
6758 `(("pkg-config" ,pkg-config)))
6759 (home-page "http://www.sbml.org")
6760 (synopsis "R support for SBML")
6762 "This package provides an R interface to libsbml for SBML parsing,
6763 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
6764 (license license:artistic2.0)))
6766 (define-public r-hypergraph
6768 (name "r-hypergraph")
6773 (uri (bioconductor-uri "hypergraph" version))
6776 "1bixmslxy7r987zw1vf4dg72hfi04lf4vj03n7ygym2g8nfhbh7m"))))
6777 (properties `((upstream-name . "hypergraph")))
6778 (build-system r-build-system)
6780 `(("r-graph" ,r-graph)))
6781 (home-page "https://bioconductor.org/packages/hypergraph")
6782 (synopsis "Hypergraph data structures")
6784 "This package implements some simple capabilities for representing and
6785 manipulating hypergraphs.")
6786 (license license:artistic2.0)))
6788 (define-public r-hyperdraw
6790 (name "r-hyperdraw")
6795 (uri (bioconductor-uri "hyperdraw" version))
6798 "0a8h3pb7196qi49ady8ni92m5wqb1hvxw6khk9j63mwj3h7jinbj"))))
6799 (properties `((upstream-name . "hyperdraw")))
6800 (build-system r-build-system)
6801 (inputs `(("graphviz" ,graphviz)))
6803 `(("r-graph" ,r-graph)
6804 ("r-hypergraph" ,r-hypergraph)
6805 ("r-rgraphviz" ,r-rgraphviz)))
6806 (home-page "https://bioconductor.org/packages/hyperdraw")
6807 (synopsis "Visualizing hypergraphs")
6809 "This package provides functions for visualizing hypergraphs.")
6810 (license license:gpl2+)))
6812 (define-public r-biggr
6819 (uri (bioconductor-uri "BiGGR" version))
6822 "1n2ypc84abmhn6br0yi87k7lvjc11k7abzhgvzdabc2ai1qgcqif"))))
6823 (properties `((upstream-name . "BiGGR")))
6824 (build-system r-build-system)
6826 `(("r-hyperdraw" ,r-hyperdraw)
6827 ("r-hypergraph" ,r-hypergraph)
6829 ("r-limsolve" ,r-limsolve)
6830 ("r-rsbml" ,r-rsbml)
6831 ("r-stringr" ,r-stringr)))
6832 (home-page "https://bioconductor.org/packages/BiGGR/")
6833 (synopsis "Constraint based modeling using metabolic reconstruction databases")
6835 "This package provides an interface to simulate metabolic reconstruction
6836 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
6837 reconstruction databases. The package facilitates @dfn{flux balance
6838 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
6839 networks and estimated fluxes can be visualized with hypergraphs.")
6840 (license license:gpl3+)))
6842 (define-public r-bigmemoryextras
6844 (name "r-bigmemoryextras")
6849 (uri (bioconductor-uri "bigmemoryExtras" version))
6852 "17dk7c44ikphcrpi8hnxyvlmj30qmj098kc0ihfi69bp9rw1cibq"))))
6854 `((upstream-name . "bigmemoryExtras")))
6855 (build-system r-build-system)
6857 `(("r-bigmemory" ,r-bigmemory)))
6858 (home-page "https://github.com/phaverty/bigmemoryExtras")
6859 (synopsis "Extension of the bigmemory package")
6861 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
6862 safety and convenience features to the @code{filebacked.big.matrix} class from
6863 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
6864 monitoring and gracefully restoring the connection to on-disk data and it also
6865 protects against accidental data modification with a filesystem-based
6866 permissions system. Utilities are provided for using @code{BigMatrix}-derived
6867 classes as @code{assayData} matrices within the @code{Biobase} package's
6868 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
6869 related to attaching to, and indexing into, file-backed matrices with
6870 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
6871 a file-backed matrix with factor properties.")
6872 (license license:artistic2.0)))
6874 (define-public r-bigpint
6881 (uri (bioconductor-uri "bigPint" version))
6884 "10vs0lzfyxp6sm4r9pxfwipjvzmmaqnvwn1hc5q37s5qz44fg0hk"))))
6885 (properties `((upstream-name . "bigPint")))
6886 (build-system r-build-system)
6888 `(("r-dplyr" ,r-dplyr)
6889 ("r-ggally" ,r-ggally)
6890 ("r-ggplot2" ,r-ggplot2)
6891 ("r-gridextra" ,r-gridextra)
6892 ("r-hexbin" ,r-hexbin)
6893 ("r-hmisc" ,r-hmisc)
6894 ("r-htmlwidgets" ,r-htmlwidgets)
6895 ("r-plotly" ,r-plotly)
6897 ("r-rcolorbrewer" ,r-rcolorbrewer)
6898 ("r-reshape" ,r-reshape)
6899 ("r-shiny" ,r-shiny)
6900 ("r-shinycssloaders" ,r-shinycssloaders)
6901 ("r-shinydashboard" ,r-shinydashboard)
6902 ("r-stringr" ,r-stringr)
6903 ("r-tidyr" ,r-tidyr)))
6904 (home-page "https://github.com/lindsayrutter/bigPint")
6905 (synopsis "Big multivariate data plotted interactively")
6907 "This package provides methods for visualizing large multivariate
6908 datasets using static and interactive scatterplot matrices, parallel
6909 coordinate plots, volcano plots, and litre plots. It includes examples for
6910 visualizing RNA-sequencing datasets and differentially expressed genes.")
6911 (license license:gpl3)))
6913 (define-public r-chemminer
6915 (name "r-chemminer")
6920 (uri (bioconductor-uri "ChemmineR" version))
6923 "1j6vmkhc03dmmkm5wgbcv62pw5dclp49f906xkx1pwg27bdldbga"))))
6924 (properties `((upstream-name . "ChemmineR")))
6925 (build-system r-build-system)
6927 `(("r-base64enc" ,r-base64enc)
6929 ("r-biocgenerics" ,r-biocgenerics)
6931 ("r-digest" ,r-digest)
6933 ("r-ggplot2" ,r-ggplot2)
6934 ("r-gridextra" ,r-gridextra)
6937 ("r-rcurl" ,r-rcurl)
6938 ("r-rjson" ,r-rjson)
6939 ("r-rsvg" ,r-rsvg)))
6940 (home-page "https://github.com/girke-lab/ChemmineR")
6941 (synopsis "Cheminformatics toolkit for R")
6943 "ChemmineR is a cheminformatics package for analyzing drug-like small
6944 molecule data in R. It contains functions for efficient processing of large
6945 numbers of molecules, physicochemical/structural property predictions,
6946 structural similarity searching, classification and clustering of compound
6947 libraries with a wide spectrum of algorithms. In addition, it offers
6948 visualization functions for compound clustering results and chemical
6950 (license license:artistic2.0)))
6952 (define-public r-bioassayr
6954 (name "r-bioassayr")
6959 (uri (bioconductor-uri "bioassayR" version))
6962 "08vxkvxhqnryfbj4dwk3ifb9pn544www9zk2pj9fjbh5xfpwi7zw"))))
6963 (properties `((upstream-name . "bioassayR")))
6964 (build-system r-build-system)
6966 `(("r-biocgenerics" ,r-biocgenerics)
6967 ("r-chemminer" ,r-chemminer)
6969 ("r-matrix" ,r-matrix)
6970 ("r-rjson" ,r-rjson)
6971 ("r-rsqlite" ,r-rsqlite)
6973 (home-page "https://github.com/TylerBackman/bioassayR")
6974 (synopsis "Cross-target analysis of small molecule bioactivity")
6976 "bioassayR is a computational tool that enables simultaneous analysis of
6977 thousands of bioassay experiments performed over a diverse set of compounds
6978 and biological targets. Unique features include support for large-scale
6979 cross-target analyses of both public and custom bioassays, generation of
6980 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
6981 preloaded database that provides access to a substantial portion of publicly
6982 available bioactivity data.")
6983 (license license:artistic2.0)))
6985 (define-public r-biobroom
6992 (uri (bioconductor-uri "biobroom" version))
6995 "1480ycdsh9xdhbpr47vdw5g6m8arqsnp8hc19wwhzm8npxh4qqlb"))))
6996 (properties `((upstream-name . "biobroom")))
6997 (build-system r-build-system)
6999 `(("r-biobase" ,r-biobase)
7000 ("r-broom" ,r-broom)
7001 ("r-dplyr" ,r-dplyr)
7002 ("r-tidyr" ,r-tidyr)))
7003 (home-page "https://github.com/StoreyLab/biobroom")
7004 (synopsis "Turn Bioconductor objects into tidy data frames")
7006 "This package contains methods for converting standard objects
7007 constructed by bioinformatics packages, especially those in Bioconductor, and
7008 converting them to @code{tidy} data. It thus serves as a complement to the
7009 @code{broom} package, and follows the same tidy, augment, glance division of
7010 tidying methods. Tidying data makes it easy to recombine, reshape and
7011 visualize bioinformatics analyses.")
7012 ;; Any version of the LGPL.
7013 (license license:lgpl3+)))
7015 (define-public r-graphite
7022 (uri (bioconductor-uri "graphite" version))
7025 "1r9fk0cpdwm7012pa85dkjcpkml2j89zcznpf4hfdz66anfyyycd"))))
7026 (properties `((upstream-name . "graphite")))
7027 (build-system r-build-system)
7029 `(("r-annotationdbi" ,r-annotationdbi)
7030 ("r-checkmate" ,r-checkmate)
7031 ("r-graph" ,r-graph)
7033 ("r-rappdirs" ,r-rappdirs)))
7034 (home-page "https://bioconductor.org/packages/graphite/")
7035 (synopsis "Networks from pathway databases")
7037 "Graphite provides networks derived from eight public pathway databases,
7038 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
7040 (license license:agpl3+)))
7042 (define-public r-reactomepa
7044 (name "r-reactomepa")
7049 (uri (bioconductor-uri "ReactomePA" version))
7052 "1vwc9kj1l4yi7c4f4lnq0i3wl2nrmmhcxyakz8qak122fi92z3j1"))))
7053 (properties `((upstream-name . "ReactomePA")))
7054 (build-system r-build-system)
7056 `(("r-annotationdbi" ,r-annotationdbi)
7058 ("r-enrichplot" ,r-enrichplot)
7059 ("r-ggplot2" ,r-ggplot2)
7060 ("r-ggraph" ,r-ggraph)
7061 ("r-graphite" ,r-graphite)
7062 ("r-igraph" ,r-igraph)
7063 ("r-reactome-db" ,r-reactome-db)))
7064 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
7065 (synopsis "Reactome pathway analysis")
7067 "This package provides functions for pathway analysis based on the
7068 REACTOME pathway database. It implements enrichment analysis, gene set
7069 enrichment analysis and several functions for visualization.")
7070 (license license:gpl2)))
7072 (define-public r-ebarrays
7079 (uri (bioconductor-uri "EBarrays" version))
7082 "063rhsdp8x0f881kslq06zxfp6b2qabrz4vmfrn8a4v3pd3n7s13"))))
7083 (properties `((upstream-name . "EBarrays")))
7084 (build-system r-build-system)
7086 `(("r-biobase" ,r-biobase)
7087 ("r-cluster" ,r-cluster)
7088 ("r-lattice" ,r-lattice)))
7089 (home-page "https://bioconductor.org/packages/EBarrays/")
7090 (synopsis "Gene clustering and differential expression identification")
7092 "EBarrays provides tools for the analysis of replicated/unreplicated
7094 (license license:gpl2+)))
7096 (define-public r-bioccasestudies
7098 (name "r-bioccasestudies")
7103 (uri (bioconductor-uri "BiocCaseStudies" version))
7106 "1sg9vxs24zfz3dg9y0qlrdsq43y0pbahbvcfxzlxjzjw80xzxpbd"))))
7108 `((upstream-name . "BiocCaseStudies")))
7109 (build-system r-build-system)
7110 (propagated-inputs `(("r-biobase" ,r-biobase)))
7111 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
7112 (synopsis "Support for the case studies monograph")
7114 "This package provides software and data to support the case studies
7116 (license license:artistic2.0)))
7118 (define-public r-biocgraph
7120 (name "r-biocgraph")
7125 (uri (bioconductor-uri "biocGraph" version))
7128 "1rv2lwiqwg7h7za23n896fs4dpla3xhw6kzwghb6iw5nlm2m61yw"))))
7129 (properties `((upstream-name . "biocGraph")))
7130 (build-system r-build-system)
7132 `(("r-biocgenerics" ,r-biocgenerics)
7133 ("r-geneplotter" ,r-geneplotter)
7134 ("r-graph" ,r-graph)
7135 ("r-rgraphviz" ,r-rgraphviz)))
7136 (home-page "https://bioconductor.org/packages/biocGraph/")
7137 (synopsis "Graph examples and use cases in Bioinformatics")
7139 "This package provides examples and code that make use of the
7140 different graph related packages produced by Bioconductor.")
7141 (license license:artistic2.0)))
7143 (define-public r-experimenthub
7145 (name "r-experimenthub")
7150 (uri (bioconductor-uri "ExperimentHub" version))
7153 "054w2lkyirbmhgia0rp4nk9zzw3zphz6jxg6fc9zlarp90g64z24"))))
7154 (properties `((upstream-name . "ExperimentHub")))
7155 (build-system r-build-system)
7157 `(("r-annotationhub" ,r-annotationhub)
7158 ("r-biocfilecache" ,r-biocfilecache)
7159 ("r-biocgenerics" ,r-biocgenerics)
7160 ("r-biocmanager" ,r-biocmanager)
7162 ("r-rappdirs" ,r-rappdirs)
7163 ("r-s4vectors" ,r-s4vectors)))
7164 (home-page "https://bioconductor.org/packages/ExperimentHub/")
7165 (synopsis "Client to access ExperimentHub resources")
7167 "This package provides a client for the Bioconductor ExperimentHub web
7168 resource. ExperimentHub provides a central location where curated data from
7169 experiments, publications or training courses can be accessed. Each resource
7170 has associated metadata, tags and date of modification. The client creates
7171 and manages a local cache of files retrieved enabling quick and reproducible
7173 (license license:artistic2.0)))
7175 (define-public r-multiassayexperiment
7177 (name "r-multiassayexperiment")
7182 (uri (bioconductor-uri "MultiAssayExperiment" version))
7185 "0hqg0b0hd5msnb4jcn1nbfyy1n1llfkipy2ivwncivkmbdn8psp4"))))
7187 `((upstream-name . "MultiAssayExperiment")))
7188 (build-system r-build-system)
7190 `(("r-biobase" ,r-biobase)
7191 ("r-biocgenerics" ,r-biocgenerics)
7192 ("r-genomicranges" ,r-genomicranges)
7193 ("r-iranges" ,r-iranges)
7194 ("r-s4vectors" ,r-s4vectors)
7195 ("r-summarizedexperiment" ,r-summarizedexperiment)
7196 ("r-tidyr" ,r-tidyr)))
7197 (home-page "http://waldronlab.io/MultiAssayExperiment/")
7198 (synopsis "Integration of multi-omics experiments in Bioconductor")
7200 "MultiAssayExperiment harmonizes data management of multiple assays
7201 performed on an overlapping set of specimens. It provides a familiar
7202 Bioconductor user experience by extending concepts from
7203 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
7204 classes for individual assays, and allowing subsetting by genomic ranges or
7206 (license license:artistic2.0)))
7208 (define-public r-bioconcotk
7210 (name "r-bioconcotk")
7215 (uri (bioconductor-uri "BiocOncoTK" version))
7218 "0rnah6c01a33yb9663jim9iclan61rpcwprb56mykgn1pf5hywbj"))))
7219 (properties `((upstream-name . "BiocOncoTK")))
7220 (build-system r-build-system)
7222 `(("r-bigrquery" ,r-bigrquery)
7224 ("r-complexheatmap" ,r-complexheatmap)
7225 ("r-curatedtcgadata" ,r-curatedtcgadata)
7227 ("r-dplyr" ,r-dplyr)
7229 ("r-genomicfeatures" ,r-genomicfeatures)
7230 ("r-genomicranges" ,r-genomicranges)
7231 ("r-ggplot2" ,r-ggplot2)
7232 ("r-ggpubr" ,r-ggpubr)
7233 ("r-graph" ,r-graph)
7235 ("r-iranges" ,r-iranges)
7236 ("r-magrittr" ,r-magrittr)
7238 ("r-rgraphviz" ,r-rgraphviz)
7239 ("r-rjson" ,r-rjson)
7240 ("r-s4vectors" ,r-s4vectors)
7241 ("r-scales" ,r-scales)
7242 ("r-shiny" ,r-shiny)
7243 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7244 (home-page "https://bioconductor.org/packages/BiocOncoTK")
7245 (synopsis "Bioconductor components for general cancer genomics")
7247 "The purpose of this package is to provide a central interface to various
7248 tools for genome-scale analysis of cancer studies.")
7249 (license license:artistic2.0)))
7251 (define-public r-biocor
7258 (uri (bioconductor-uri "BioCor" version))
7261 "1bjw02rwmz2d715sgpfp08njb15200ch7cmipsf9hd5835ppg1jl"))))
7262 (properties `((upstream-name . "BioCor")))
7263 (build-system r-build-system)
7265 `(("r-biocparallel" ,r-biocparallel)
7266 ("r-gseabase" ,r-gseabase)
7267 ("r-matrix" ,r-matrix)))
7268 (home-page "https://llrs.github.io/BioCor/")
7269 (synopsis "Functional similarities")
7271 "This package provides tools to calculate functional similarities based
7272 on the pathways described on KEGG and REACTOME or in gene sets. These
7273 similarities can be calculated for pathways or gene sets, genes, or clusters
7274 and combined with other similarities. They can be used to improve networks,
7275 gene selection, testing relationships, and so on.")
7276 (license license:expat)))
7278 (define-public r-biocpkgtools
7280 (name "r-biocpkgtools")
7285 (uri (bioconductor-uri "BiocPkgTools" version))
7288 "0gyhb3071pxmvaxla7cxy9k97s3z3ynl62jnqz9jnkd53c7jnd53"))))
7289 (properties `((upstream-name . "BiocPkgTools")))
7290 (build-system r-build-system)
7292 `(("r-biocmanager" ,r-biocmanager)
7293 ("r-biocviews" ,r-biocviews)
7294 ("r-dplyr" ,r-dplyr)
7297 ("r-graph" ,r-graph)
7298 ("r-htmltools" ,r-htmltools)
7299 ("r-htmlwidgets" ,r-htmlwidgets)
7301 ("r-igraph" ,r-igraph)
7302 ("r-jsonlite" ,r-jsonlite)
7303 ("r-magrittr" ,r-magrittr)
7305 ("r-readr" ,r-readr)
7307 ("r-rvest" ,r-rvest)
7308 ("r-stringr" ,r-stringr)
7309 ("r-tibble" ,r-tibble)
7310 ("r-tidyr" ,r-tidyr)
7311 ("r-xml2" ,r-xml2)))
7312 (home-page "https://github.com/seandavi/BiocPkgTools")
7313 (synopsis "Collection of tools for learning about Bioconductor packages")
7315 "Bioconductor has a rich ecosystem of metadata around packages, usage,
7316 and build status. This package is a simple collection of functions to access
7317 that metadata from R. The goal is to expose metadata for data mining and
7318 value-added functionality such as package searching, text mining, and
7319 analytics on packages.")
7320 (license license:expat)))