1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018, 2020 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>
6 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
7 ;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
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14 ;;; your option) any later version.
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17 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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19 ;;; GNU General Public License for more details.
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22 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
24 (define-module (gnu packages bioconductor)
25 #:use-module ((guix licenses) #:prefix license:)
26 #:use-module (guix packages)
27 #:use-module (guix download)
28 #:use-module (guix git-download)
29 #:use-module (guix build-system r)
30 #:use-module (gnu packages)
31 #:use-module (gnu packages base)
32 #:use-module (gnu packages bioinformatics)
33 #:use-module (gnu packages cran)
34 #:use-module (gnu packages compression)
35 #:use-module (gnu packages gcc)
36 #:use-module (gnu packages graph)
37 #:use-module (gnu packages graphviz)
38 #:use-module (gnu packages haskell-xyz)
39 #:use-module (gnu packages image)
40 #:use-module (gnu packages maths)
41 #:use-module (gnu packages netpbm)
42 #:use-module (gnu packages perl)
43 #:use-module (gnu packages pkg-config)
44 #:use-module (gnu packages statistics)
45 #:use-module (gnu packages web)
46 #:use-module (gnu packages xml)
47 #:use-module (srfi srfi-1))
52 (define-public r-reactome-db
54 (name "r-reactome-db")
59 (uri (bioconductor-uri "reactome.db" version 'annotation))
62 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
63 (properties `((upstream-name . "reactome.db")))
64 (build-system r-build-system)
66 `(("r-annotationdbi" ,r-annotationdbi)))
67 (home-page "https://bioconductor.org/packages/reactome.db/")
68 (synopsis "Annotation maps for reactome")
70 "This package provides a set of annotation maps for the REACTOME
71 database, assembled using data from REACTOME.")
72 (license license:cc-by4.0)))
74 (define-public r-bsgenome-celegans-ucsc-ce6
76 (name "r-bsgenome-celegans-ucsc-ce6")
80 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
84 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
86 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
87 (build-system r-build-system)
89 `(("r-bsgenome" ,r-bsgenome)))
91 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
92 (synopsis "Full genome sequences for Worm")
94 "This package provides full genome sequences for Caenorhabditis
95 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
97 (license license:artistic2.0)))
99 (define-public r-bsgenome-celegans-ucsc-ce10
101 (name "r-bsgenome-celegans-ucsc-ce10")
105 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
106 version 'annotation))
109 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
111 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
112 (build-system r-build-system)
114 `(("r-bsgenome" ,r-bsgenome)))
116 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
117 (synopsis "Full genome sequences for Worm")
119 "This package provides full genome sequences for Caenorhabditis
120 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
122 (license license:artistic2.0)))
124 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
126 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
130 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
131 version 'annotation))
134 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
136 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
137 (build-system r-build-system)
139 `(("r-bsgenome" ,r-bsgenome)))
141 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
142 (synopsis "Full genome sequences for Fly")
144 "This package provides full genome sequences for Drosophila
145 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
147 (license license:artistic2.0)))
149 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
151 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
155 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
156 version 'annotation))
159 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
161 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
162 (build-system r-build-system)
164 `(("r-bsgenome" ,r-bsgenome)))
166 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
167 (synopsis "Full genome sequences for Fly")
169 "This package provides full genome sequences for Drosophila
170 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
171 Biostrings objects.")
172 (license license:artistic2.0)))
174 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
176 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
180 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
181 version 'annotation))
184 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
186 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
187 (build-system r-build-system)
189 `(("r-bsgenome" ,r-bsgenome)
190 ("r-bsgenome-dmelanogaster-ucsc-dm3"
191 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
192 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
193 (synopsis "Full masked genome sequences for Fly")
195 "This package provides full masked genome sequences for Drosophila
196 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
197 Biostrings objects. The sequences are the same as in
198 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
199 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
200 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
201 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
202 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
203 (license license:artistic2.0)))
205 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
207 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
211 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
212 version 'annotation))
215 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
217 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
218 (build-system r-build-system)
220 `(("r-bsgenome" ,r-bsgenome)))
222 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
223 (synopsis "Full genome sequences for Homo sapiens")
225 "This package provides full genome sequences for Homo sapiens from
226 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
227 (license license:artistic2.0)))
229 (define-public r-bsgenome-hsapiens-ncbi-grch38
231 (name "r-bsgenome-hsapiens-ncbi-grch38")
236 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
237 version 'annotation))
240 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
241 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
242 (build-system r-build-system)
243 (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
245 "https://bioconductor.org/packages/release/data/annotation/html/\
246 BSgenome.Hsapiens.NCBI.GRCh38.html")
247 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
249 "This package provides full genome sequences for Homo sapiens (Human) as
250 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
251 (license license:artistic2.0)))
253 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
255 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
259 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
260 version 'annotation))
263 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
265 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
266 (build-system r-build-system)
268 `(("r-bsgenome" ,r-bsgenome)
269 ("r-bsgenome-hsapiens-ucsc-hg19"
270 ,r-bsgenome-hsapiens-ucsc-hg19)))
271 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
272 (synopsis "Full masked genome sequences for Homo sapiens")
274 "This package provides full genome sequences for Homo sapiens (Human) as
275 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
276 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
277 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
278 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
279 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
280 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
282 (license license:artistic2.0)))
284 (define-public r-bsgenome-mmusculus-ucsc-mm9
286 (name "r-bsgenome-mmusculus-ucsc-mm9")
290 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
291 version 'annotation))
294 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
296 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
297 (build-system r-build-system)
299 `(("r-bsgenome" ,r-bsgenome)))
301 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
302 (synopsis "Full genome sequences for Mouse")
304 "This package provides full genome sequences for Mus musculus (Mouse) as
305 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
306 (license license:artistic2.0)))
308 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
310 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
314 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
315 version 'annotation))
318 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
320 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
321 (build-system r-build-system)
323 `(("r-bsgenome" ,r-bsgenome)
324 ("r-bsgenome-mmusculus-ucsc-mm9"
325 ,r-bsgenome-mmusculus-ucsc-mm9)))
326 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
327 (synopsis "Full masked genome sequences for Mouse")
329 "This package provides full genome sequences for Mus musculus (Mouse) as
330 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
331 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
332 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
333 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
334 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
335 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
337 (license license:artistic2.0)))
339 (define-public r-bsgenome-mmusculus-ucsc-mm10
341 (name "r-bsgenome-mmusculus-ucsc-mm10")
345 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
346 version 'annotation))
349 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
351 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
352 (build-system r-build-system)
354 `(("r-bsgenome" ,r-bsgenome)))
356 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
357 (synopsis "Full genome sequences for Mouse")
359 "This package provides full genome sequences for Mus
360 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
361 in Biostrings objects.")
362 (license license:artistic2.0)))
364 (define-public r-org-ce-eg-db
366 (name "r-org-ce-eg-db")
370 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
373 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
375 `((upstream-name . "org.Ce.eg.db")))
376 (build-system r-build-system)
378 `(("r-annotationdbi" ,r-annotationdbi)))
379 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
380 (synopsis "Genome wide annotation for Worm")
382 "This package provides mappings from Entrez gene identifiers to various
383 annotations for the genome of the model worm Caenorhabditis elegans.")
384 (license license:artistic2.0)))
386 (define-public r-org-dm-eg-db
388 (name "r-org-dm-eg-db")
392 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
395 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
397 `((upstream-name . "org.Dm.eg.db")))
398 (build-system r-build-system)
400 `(("r-annotationdbi" ,r-annotationdbi)))
401 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
402 (synopsis "Genome wide annotation for Fly")
404 "This package provides mappings from Entrez gene identifiers to various
405 annotations for the genome of the model fruit fly Drosophila melanogaster.")
406 (license license:artistic2.0)))
408 (define-public r-org-dr-eg-db
410 (name "r-org-dr-eg-db")
414 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
417 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
419 `((upstream-name . "org.Dr.eg.db")))
420 (build-system r-build-system)
422 `(("r-annotationdbi" ,r-annotationdbi)))
423 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
424 (synopsis "Annotation for Zebrafish")
426 "This package provides genome wide annotations for Zebrafish, primarily
427 based on mapping using Entrez Gene identifiers.")
428 (license license:artistic2.0)))
430 (define-public r-org-hs-eg-db
432 (name "r-org-hs-eg-db")
436 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
439 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
441 `((upstream-name . "org.Hs.eg.db")))
442 (build-system r-build-system)
444 `(("r-annotationdbi" ,r-annotationdbi)))
445 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
446 (synopsis "Genome wide annotation for Human")
448 "This package contains genome-wide annotations for Human, primarily based
449 on mapping using Entrez Gene identifiers.")
450 (license license:artistic2.0)))
452 (define-public r-org-mm-eg-db
454 (name "r-org-mm-eg-db")
458 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
461 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
463 `((upstream-name . "org.Mm.eg.db")))
464 (build-system r-build-system)
466 `(("r-annotationdbi" ,r-annotationdbi)))
467 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
468 (synopsis "Genome wide annotation for Mouse")
470 "This package provides mappings from Entrez gene identifiers to various
471 annotations for the genome of the model mouse Mus musculus.")
472 (license license:artistic2.0)))
474 (define-public r-bsgenome-hsapiens-ucsc-hg19
476 (name "r-bsgenome-hsapiens-ucsc-hg19")
480 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
481 version 'annotation))
484 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
486 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
487 (build-system r-build-system)
489 `(("r-bsgenome" ,r-bsgenome)))
491 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
492 (synopsis "Full genome sequences for Homo sapiens")
494 "This package provides full genome sequences for Homo sapiens as provided
495 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
496 (license license:artistic2.0)))
498 (define-public r-bsgenome-hsapiens-ucsc-hg38
500 (name "r-bsgenome-hsapiens-ucsc-hg38")
504 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
505 version 'annotation))
508 "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
510 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
511 (build-system r-build-system)
513 `(("r-bsgenome" ,r-bsgenome)))
515 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
516 (synopsis "Full genome sequences for Homo sapiens")
518 "This package provides full genome sequences for Homo sapiens (Human)
519 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
520 (license license:artistic2.0)))
522 (define-public r-ensdb-hsapiens-v75
524 (name "r-ensdb-hsapiens-v75")
529 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
532 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
534 `((upstream-name . "EnsDb.Hsapiens.v75")))
535 (build-system r-build-system)
537 `(("r-ensembldb" ,r-ensembldb)))
538 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
539 (synopsis "Ensembl based annotation package")
541 "This package exposes an annotation database generated from Ensembl.")
542 (license license:artistic2.0)))
544 (define-public r-genelendatabase
546 (name "r-genelendatabase")
551 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
554 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
556 `((upstream-name . "geneLenDataBase")))
557 (build-system r-build-system)
559 `(("r-rtracklayer" ,r-rtracklayer)
560 ("r-genomicfeatures" ,r-genomicfeatures)))
561 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
562 (synopsis "Lengths of mRNA transcripts for a number of genomes")
564 "This package provides the lengths of mRNA transcripts for a number of
565 genomes and gene ID formats, largely based on the UCSC table browser.")
566 (license license:lgpl2.0+)))
568 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
570 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
574 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
575 version 'annotation))
578 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
580 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
581 (build-system r-build-system)
583 `(("r-genomicfeatures" ,r-genomicfeatures)))
585 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
586 (synopsis "Annotation package for human genome in TxDb format")
588 "This package provides an annotation database of Homo sapiens genome
589 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
590 track. The database is exposed as a @code{TxDb} object.")
591 (license license:artistic2.0)))
593 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
595 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
599 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
600 version 'annotation))
603 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
605 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
606 (build-system r-build-system)
608 `(("r-genomicfeatures" ,r-genomicfeatures)))
610 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
611 (synopsis "Annotation package for human genome in TxDb format")
613 "This package provides an annotation database of Homo sapiens genome
614 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
615 track. The database is exposed as a @code{TxDb} object.")
616 (license license:artistic2.0)))
618 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
620 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
624 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
625 version 'annotation))
628 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
630 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
631 (build-system r-build-system)
633 `(("r-genomicfeatures" ,r-genomicfeatures)
634 ("r-annotationdbi" ,r-annotationdbi)))
636 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
637 (synopsis "Annotation package for mouse genome in TxDb format")
639 "This package provides an annotation database of Mouse genome data. It
640 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
641 database is exposed as a @code{TxDb} object.")
642 (license license:artistic2.0)))
644 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
646 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
650 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
651 version 'annotation))
654 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
656 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
657 (build-system r-build-system)
659 `(("r-bsgenome" ,r-bsgenome)
660 ("r-genomicfeatures" ,r-genomicfeatures)
661 ("r-annotationdbi" ,r-annotationdbi)))
663 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
664 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
666 "This package loads a TxDb object, which is an R interface to
667 prefabricated databases contained in this package. This package provides
668 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
669 based on the knownGene track.")
670 (license license:artistic2.0)))
672 (define-public r-txdb-celegans-ucsc-ce6-ensgene
674 (name "r-txdb-celegans-ucsc-ce6-ensgene")
679 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
680 version 'annotation))
683 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
685 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
686 (build-system r-build-system)
688 `(("r-annotationdbi" ,r-annotationdbi)
689 ("r-genomicfeatures" ,r-genomicfeatures)))
690 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
691 (synopsis "Annotation package for C elegans TxDb objects")
693 "This package exposes a C elegans annotation database generated from UCSC
694 by exposing these as TxDb objects.")
695 (license license:artistic2.0)))
697 (define-public r-fdb-infiniummethylation-hg19
699 (name "r-fdb-infiniummethylation-hg19")
703 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
704 version 'annotation))
707 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
709 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
710 (build-system r-build-system)
712 `(("r-biostrings" ,r-biostrings)
713 ("r-genomicfeatures" ,r-genomicfeatures)
714 ("r-annotationdbi" ,r-annotationdbi)
715 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
716 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
717 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
718 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
720 "This is an annotation package for Illumina Infinium DNA methylation
721 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
723 (license license:artistic2.0)))
725 (define-public r-illuminahumanmethylationepicmanifest
727 (name "r-illuminahumanmethylationepicmanifest")
731 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
732 version 'annotation))
735 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
737 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
738 (build-system r-build-system)
740 `(("r-minfi" ,r-minfi)))
741 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
742 (synopsis "Manifest for Illumina's EPIC methylation arrays")
744 "This is a manifest package for Illumina's EPIC methylation arrays.")
745 (license license:artistic2.0)))
747 (define-public r-ideoviz
753 (uri (bioconductor-uri "IdeoViz" version))
756 "1ndj14qhpgidjb4qsga80ghqzz1x8kvy2gy1bvvgwlkfxa62rn50"))))
757 (build-system r-build-system)
759 `(("r-biobase" ,r-biobase)
760 ("r-iranges" ,r-iranges)
761 ("r-genomicranges" ,r-genomicranges)
762 ("r-rcolorbrewer" ,r-rcolorbrewer)
763 ("r-rtracklayer" ,r-rtracklayer)
764 ("r-genomeinfodb" ,r-genomeinfodb)))
765 (home-page "https://bioconductor.org/packages/IdeoViz/")
766 (synopsis "Plots data along a chromosomal ideogram")
767 (description "This package provides functions to plot data associated with
768 arbitrary genomic intervals along chromosomal ideogram.")
769 (license license:gpl2)))
771 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
772 ;; from Bioconductor.
773 (define-public r-deconstructsigs
775 (name "r-deconstructsigs")
779 (uri (cran-uri "deconstructSigs" version))
782 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
784 `((upstream-name . "deconstructSigs")))
785 (build-system r-build-system)
787 `(("r-bsgenome" ,r-bsgenome)
788 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
789 ("r-genomeinfodb" ,r-genomeinfodb)
790 ("r-reshape2" ,r-reshape2)))
791 (home-page "https://github.com/raerose01/deconstructSigs")
792 (synopsis "Identifies signatures present in a tumor sample")
793 (description "This package takes sample information in the form of the
794 fraction of mutations in each of 96 trinucleotide contexts and identifies
795 the weighted combination of published signatures that, when summed, most
796 closely reconstructs the mutational profile.")
797 (license license:gpl2+)))
799 ;; This is a CRAN package, but it depends on Bioconductor packages.
807 (uri (cran-uri "NMF" version))
810 "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g"))))
811 (properties `((upstream-name . "NMF")))
812 (build-system r-build-system)
814 `(("r-cluster" ,r-cluster)
815 ("r-biobase" ,r-biobase)
816 ("r-biocmanager" ,r-biocmanager)
817 ("r-bigmemory" ,r-bigmemory) ; suggested
818 ("r-synchronicity" ,r-synchronicity) ; suggested
819 ("r-colorspace" ,r-colorspace)
820 ("r-digest" ,r-digest)
821 ("r-doparallel" ,r-doparallel)
822 ("r-foreach" ,r-foreach)
823 ("r-ggplot2" ,r-ggplot2)
824 ("r-gridbase" ,r-gridbase)
825 ("r-pkgmaker" ,r-pkgmaker)
826 ("r-rcolorbrewer" ,r-rcolorbrewer)
827 ("r-registry" ,r-registry)
828 ("r-reshape2" ,r-reshape2)
829 ("r-rngtools" ,r-rngtools)
830 ("r-stringr" ,r-stringr)))
832 `(("r-knitr" ,r-knitr)))
833 (home-page "http://renozao.github.io/NMF")
834 (synopsis "Algorithms and framework for nonnegative matrix factorization")
836 "This package provides a framework to perform Non-negative Matrix
837 Factorization (NMF). The package implements a set of already published
838 algorithms and seeding methods, and provides a framework to test, develop and
839 plug new or custom algorithms. Most of the built-in algorithms have been
840 optimized in C++, and the main interface function provides an easy way of
841 performing parallel computations on multicore machines.")
842 (license license:gpl2+)))
844 (define-public r-do-db
850 (uri (bioconductor-uri "DO.db" version 'annotation))
853 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
855 `((upstream-name . "DO.db")))
856 (build-system r-build-system)
858 `(("r-annotationdbi" ,r-annotationdbi)))
859 (home-page "https://www.bioconductor.org/packages/DO.db/")
860 (synopsis "Annotation maps describing the entire Disease Ontology")
862 "This package provides a set of annotation maps describing the entire
864 (license license:artistic2.0)))
866 (define-public r-pasilla
873 "http://bioconductor.org/packages/release/data/experiment"
874 "/src/contrib/pasilla_" version ".tar.gz"))
877 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
878 (build-system r-build-system)
880 `(("r-biocstyle" ,r-biocstyle)
881 ("r-dexseq" ,r-dexseq)
883 ("r-rmarkdown" ,r-rmarkdown)))
884 (home-page "https://www.bioconductor.org/packages/pasilla/")
885 (synopsis "Data package with per-exon and per-gene read counts")
886 (description "This package provides per-exon and per-gene read counts
887 computed for selected genes from RNA-seq data that were presented in the
888 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
889 by Brooks et al., Genome Research 2011.")
890 (license license:lgpl2.1+)))
892 (define-public r-pfam-db
899 (uri (bioconductor-uri "PFAM.db" version 'annotation))
902 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
903 (properties `((upstream-name . "PFAM.db")))
904 (build-system r-build-system)
906 `(("r-annotationdbi" ,r-annotationdbi)))
907 (home-page "https://bioconductor.org/packages/PFAM.db")
908 (synopsis "Set of protein ID mappings for PFAM")
910 "This package provides a set of protein ID mappings for PFAM, assembled
911 using data from public repositories.")
912 (license license:artistic2.0)))
914 (define-public r-phastcons100way-ucsc-hg19
916 (name "r-phastcons100way-ucsc-hg19")
921 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
922 version 'annotation))
925 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
927 `((upstream-name . "phastCons100way.UCSC.hg19")))
928 (build-system r-build-system)
930 `(("r-bsgenome" ,r-bsgenome)
931 ("r-genomeinfodb" ,r-genomeinfodb)
932 ("r-genomicranges" ,r-genomicranges)
933 ("r-genomicscores" ,r-genomicscores)
934 ("r-iranges" ,r-iranges)
935 ("r-s4vectors" ,r-s4vectors)))
936 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
937 (synopsis "UCSC phastCons conservation scores for hg19")
939 "This package provides UCSC phastCons conservation scores for the human
940 genome (hg19) calculated from multiple alignments with other 99 vertebrate
942 (license license:artistic2.0)))
947 (define-public r-abadata
953 (uri (bioconductor-uri "ABAData" version 'experiment))
956 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
958 `((upstream-name . "ABAData")))
959 (build-system r-build-system)
961 `(("r-annotationdbi" ,r-annotationdbi)))
962 (home-page "https://www.bioconductor.org/packages/ABAData/")
963 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
965 "This package provides the data for the gene expression enrichment
966 analysis conducted in the package ABAEnrichment. The package includes three
967 datasets which are derived from the Allen Brain Atlas:
970 @item Gene expression data from Human Brain (adults) averaged across donors,
971 @item Gene expression data from the Developing Human Brain pooled into five
972 age categories and averaged across donors, and
973 @item a developmental effect score based on the Developing Human Brain
977 All datasets are restricted to protein coding genes.")
978 (license license:gpl2+)))
980 (define-public r-arrmdata
986 (uri (bioconductor-uri "ARRmData" version 'experiment))
989 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
991 `((upstream-name . "ARRmData")))
992 (build-system r-build-system)
993 (home-page "https://www.bioconductor.org/packages/ARRmData/")
994 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
996 "This package provides raw beta values from 36 samples across 3 groups
997 from Illumina 450k methylation arrays.")
998 (license license:artistic2.0)))
1000 (define-public r-hsmmsinglecell
1002 (name "r-hsmmsinglecell")
1006 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
1009 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
1011 `((upstream-name . "HSMMSingleCell")))
1012 (build-system r-build-system)
1013 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
1014 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
1016 "Skeletal myoblasts undergo a well-characterized sequence of
1017 morphological and transcriptional changes during differentiation. In this
1018 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1019 under high mitogen conditions (GM) and then differentiated by switching to
1020 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1021 hundred cells taken over a time-course of serum-induced differentiation.
1022 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1023 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1024 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1025 which were then sequenced to a depth of ~4 million reads per library,
1026 resulting in a complete gene expression profile for each cell.")
1027 (license license:artistic2.0)))
1029 (define-public r-all
1035 (uri (bioconductor-uri "ALL" version 'experiment))
1038 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
1039 (properties `((upstream-name . "ALL")))
1040 (build-system r-build-system)
1042 `(("r-biobase" ,r-biobase)))
1043 (home-page "https://bioconductor.org/packages/ALL")
1044 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1046 "The data consist of microarrays from 128 different individuals with
1047 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1048 are available. The data have been normalized (using rma) and it is the
1049 jointly normalized data that are available here. The data are presented in
1050 the form of an @code{exprSet} object.")
1051 (license license:artistic2.0)))
1053 (define-public r-affydata
1060 (uri (bioconductor-uri "affydata" version 'experiment))
1063 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
1064 (properties `((upstream-name . "affydata")))
1065 (build-system r-build-system)
1067 `(("r-affy" ,r-affy)))
1068 (home-page "https://bioconductor.org/packages/affydata/")
1069 (synopsis "Affymetrix data for demonstration purposes")
1071 "This package provides example datasets that represent 'real world
1072 examples' of Affymetrix data, unlike the artificial examples included in the
1073 package @code{affy}.")
1074 (license license:gpl2+)))
1076 (define-public r-coverageview
1078 (name "r-coverageview")
1082 (uri (bioconductor-uri "CoverageView" version))
1085 "1fcz7pkffz5l3jdxb9glji2zdmr6nx67h6vfpr2yi8n3slg2hrrj"))))
1086 (build-system r-build-system)
1088 `(("r-s4vectors" ,r-s4vectors)
1089 ("r-iranges" ,r-iranges)
1090 ("r-genomicranges" ,r-genomicranges)
1091 ("r-genomicalignments" ,r-genomicalignments)
1092 ("r-rtracklayer" ,r-rtracklayer)
1093 ("r-rsamtools" ,r-rsamtools)))
1094 (home-page "https://bioconductor.org/packages/CoverageView/")
1095 (synopsis "Coverage visualization package for R")
1096 (description "This package provides a framework for the visualization of
1097 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
1098 be also used for genome-wide nucleosome positioning experiments or other
1099 experiment types where it is important to have a framework in order to inspect
1100 how the coverage distributed across the genome.")
1101 (license license:artistic2.0)))
1103 (define-public r-cummerbund
1105 (name "r-cummerbund")
1109 (uri (bioconductor-uri "cummeRbund" version))
1112 "1av7yfxcq1wwbqfqcz7caiz5kf6kg5wq9qcg5v6yccihclzwvxjc"))))
1113 (build-system r-build-system)
1115 `(("r-biobase" ,r-biobase)
1116 ("r-biocgenerics" ,r-biocgenerics)
1117 ("r-fastcluster", r-fastcluster)
1118 ("r-ggplot2" ,r-ggplot2)
1121 ("r-reshape2" ,r-reshape2)
1122 ("r-rsqlite" ,r-rsqlite)
1123 ("r-rtracklayer" ,r-rtracklayer)
1124 ("r-s4vectors" ,r-s4vectors)))
1125 (home-page "https://bioconductor.org/packages/cummeRbund/")
1126 (synopsis "Analyze Cufflinks high-throughput sequencing data")
1127 (description "This package allows for persistent storage, access,
1128 exploration, and manipulation of Cufflinks high-throughput sequencing
1129 data. In addition, provides numerous plotting functions for commonly
1130 used visualizations.")
1131 (license license:artistic2.0)))
1133 (define-public r-curatedtcgadata
1135 (name "r-curatedtcgadata")
1140 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1143 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
1145 `((upstream-name . "curatedTCGAData")))
1146 (build-system r-build-system)
1148 `(("r-annotationhub" ,r-annotationhub)
1149 ("r-experimenthub" ,r-experimenthub)
1150 ("r-hdf5array" ,r-hdf5array)
1151 ("r-multiassayexperiment" ,r-multiassayexperiment)
1152 ("r-s4vectors" ,r-s4vectors)
1153 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1154 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1155 (synopsis "Curated data from The Cancer Genome Atlas")
1157 "This package provides publicly available data from The Cancer Genome
1158 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1159 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1160 number, mutation, microRNA, protein, and others) with clinical / pathological
1161 data. It also links assay barcodes with patient identifiers, enabling
1162 harmonized subsetting of rows (features) and columns (patients / samples)
1163 across the entire multi-'omics experiment.")
1164 (license license:artistic2.0)))
1169 (define-public r-biocversion
1171 (name "r-biocversion")
1176 (uri (bioconductor-uri "BiocVersion" version))
1179 "1rrzx3dqds0jlj1bmjc744wiamb2hssbh3jfxz1s9jp4cvnwrpmz"))))
1180 (properties `((upstream-name . "BiocVersion")))
1181 (build-system r-build-system)
1182 (home-page "https://bioconductor.org/packages/BiocVersion/")
1183 (synopsis "Set the appropriate version of Bioconductor packages")
1185 "This package provides repository information for the appropriate version
1187 (license license:artistic2.0)))
1189 (define-public r-biocgenerics
1191 (name "r-biocgenerics")
1195 (uri (bioconductor-uri "BiocGenerics" version))
1198 "15nvqyh2gx5zkn1krbs5c4rhw5642bijdfsf2rgic70gzr05cksk"))))
1200 `((upstream-name . "BiocGenerics")))
1201 (build-system r-build-system)
1202 (home-page "https://bioconductor.org/packages/BiocGenerics")
1203 (synopsis "S4 generic functions for Bioconductor")
1205 "This package provides S4 generic functions needed by many Bioconductor
1207 (license license:artistic2.0)))
1209 (define-public r-affycomp
1216 (uri (bioconductor-uri "affycomp" version))
1219 "0zg8dshas5b2ny4pnxxxqihnr4l20666ivrgglb939a23mplgps0"))))
1220 (properties `((upstream-name . "affycomp")))
1221 (build-system r-build-system)
1222 (propagated-inputs `(("r-biobase" ,r-biobase)))
1223 (home-page "https://bioconductor.org/packages/affycomp/")
1224 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1226 "The package contains functions that can be used to compare expression
1227 measures for Affymetrix Oligonucleotide Arrays.")
1228 (license license:gpl2+)))
1230 (define-public r-affycompatible
1232 (name "r-affycompatible")
1237 (uri (bioconductor-uri "AffyCompatible" version))
1240 "0394sr4spafhfypjsafwjr0y0zsgv52ajdcyvsmkdk7375898lqd"))))
1242 `((upstream-name . "AffyCompatible")))
1243 (build-system r-build-system)
1245 `(("r-biostrings" ,r-biostrings)
1246 ("r-rcurl" ,r-rcurl)
1248 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1249 (synopsis "Work with Affymetrix GeneChip files")
1251 "This package provides an interface to Affymetrix chip annotation and
1252 sample attribute files. The package allows an easy way for users to download
1253 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1254 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1255 Command Console} (AGCC)-compatible sample annotation files.")
1256 (license license:artistic2.0)))
1258 (define-public r-affycontam
1260 (name "r-affycontam")
1265 (uri (bioconductor-uri "affyContam" version))
1268 "1dh5c3blk2dl9kg13y6snplnx61x2f9hvp5lc7jmg25xk916517i"))))
1269 (properties `((upstream-name . "affyContam")))
1270 (build-system r-build-system)
1272 `(("r-affy" ,r-affy)
1273 ("r-affydata" ,r-affydata)
1274 ("r-biobase" ,r-biobase)))
1275 (home-page "https://bioconductor.org/packages/affyContam/")
1276 (synopsis "Structured corruption of Affymetrix CEL file data")
1278 "Microarray quality assessment is a major concern of microarray analysts.
1279 This package provides some simple approaches to in silico creation of quality
1280 problems in CEL-level data to help evaluate performance of quality metrics.")
1281 (license license:artistic2.0)))
1283 (define-public r-affycoretools
1285 (name "r-affycoretools")
1290 (uri (bioconductor-uri "affycoretools" version))
1293 "0cnb54b3kmg9rnycvaz949bdali9n98qzrw7gwka6abmg1lv232s"))))
1294 (properties `((upstream-name . "affycoretools")))
1295 (build-system r-build-system)
1297 `(("r-affy" ,r-affy)
1298 ("r-annotationdbi" ,r-annotationdbi)
1299 ("r-biobase" ,r-biobase)
1300 ("r-biocgenerics" ,r-biocgenerics)
1302 ("r-edger" ,r-edger)
1303 ("r-gcrma" ,r-gcrma)
1304 ("r-glimma" ,r-glimma)
1305 ("r-ggplot2" ,r-ggplot2)
1306 ("r-gostats" ,r-gostats)
1307 ("r-gplots" ,r-gplots)
1308 ("r-hwriter" ,r-hwriter)
1309 ("r-lattice" ,r-lattice)
1310 ("r-limma" ,r-limma)
1311 ("r-oligoclasses" ,r-oligoclasses)
1312 ("r-reportingtools" ,r-reportingtools)
1313 ("r-rsqlite" ,r-rsqlite)
1314 ("r-s4vectors" ,r-s4vectors)
1315 ("r-xtable" ,r-xtable)))
1317 `(("r-knitr" ,r-knitr)))
1318 (home-page "https://bioconductor.org/packages/affycoretools/")
1319 (synopsis "Functions for analyses with Affymetrix GeneChips")
1321 "This package provides various wrapper functions that have been written
1322 to streamline the more common analyses that a Biostatistician might see.")
1323 (license license:artistic2.0)))
1325 (define-public r-affxparser
1327 (name "r-affxparser")
1332 (uri (bioconductor-uri "affxparser" version))
1335 "0d4hq1w0a3dm4bg9qsv7wqrbv2y7b9gllxfmnqs9n2nnwmvgi8yq"))))
1336 (properties `((upstream-name . "affxparser")))
1337 (build-system r-build-system)
1338 (home-page "https://github.com/HenrikBengtsson/affxparser")
1339 (synopsis "Affymetrix File Parsing SDK")
1341 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1342 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1343 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1344 are supported. Currently, there are methods for reading @dfn{chip definition
1345 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1346 either in full or in part. For example, probe signals from a few probesets
1347 can be extracted very quickly from a set of CEL files into a convenient list
1349 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1351 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1353 (define-public r-annotate
1360 (uri (bioconductor-uri "annotate" version))
1363 "1ivszqknryq6n5a85z8zj12fvgcs6zz3zlza8q08pl6cs4m5rm4w"))))
1364 (build-system r-build-system)
1366 `(("r-annotationdbi" ,r-annotationdbi)
1367 ("r-biobase" ,r-biobase)
1368 ("r-biocgenerics" ,r-biocgenerics)
1370 ("r-rcurl" ,r-rcurl)
1372 ("r-xtable" ,r-xtable)))
1374 "https://bioconductor.org/packages/annotate")
1375 (synopsis "Annotation for microarrays")
1376 (description "This package provides R environments for the annotation of
1378 (license license:artistic2.0)))
1380 (define-public r-hpar
1387 (uri (bioconductor-uri "hpar" version))
1390 "1jq0qw7wq3426cp004divywjm3ryixkykcmwlhrri13agz6rx3r9"))))
1391 (build-system r-build-system)
1393 `(("r-knitr" ,r-knitr)))
1394 (home-page "https://bioconductor.org/packages/hpar/")
1395 (synopsis "Human Protein Atlas in R")
1396 (description "This package provides a simple interface to and data from
1397 the Human Protein Atlas project.")
1398 (license license:artistic2.0)))
1400 (define-public r-regioner
1407 (uri (bioconductor-uri "regioneR" version))
1410 "0bzjwzj5mvb49wgvs3gd3jfpm7s0zfkca763i65i7m994lgvz33c"))))
1411 (properties `((upstream-name . "regioneR")))
1412 (build-system r-build-system)
1414 `(("r-biostrings" ,r-biostrings)
1415 ("r-bsgenome" ,r-bsgenome)
1416 ("r-genomeinfodb" ,r-genomeinfodb)
1417 ("r-genomicranges" ,r-genomicranges)
1418 ("r-iranges" ,r-iranges)
1419 ("r-memoise" ,r-memoise)
1420 ("r-rtracklayer" ,r-rtracklayer)
1421 ("r-s4vectors" ,r-s4vectors)))
1423 `(("r-knitr" ,r-knitr)))
1424 (home-page "https://bioconductor.org/packages/regioneR/")
1425 (synopsis "Association analysis of genomic regions")
1426 (description "This package offers a statistical framework based on
1427 customizable permutation tests to assess the association between genomic
1428 region sets and other genomic features.")
1429 (license license:artistic2.0)))
1431 (define-public r-reportingtools
1433 (name "r-reportingtools")
1438 (uri (bioconductor-uri "ReportingTools" version))
1441 "1ig1h224silbdbdr0j9j9sysp9l9dzpcsjzn8jp57h3gh4pdqbfx"))))
1443 `((upstream-name . "ReportingTools")))
1444 (build-system r-build-system)
1446 `(("r-annotate" ,r-annotate)
1447 ("r-annotationdbi" ,r-annotationdbi)
1448 ("r-biobase" ,r-biobase)
1449 ("r-biocgenerics" ,r-biocgenerics)
1450 ("r-category" ,r-category)
1451 ("r-deseq2" ,r-deseq2)
1452 ("r-edger" ,r-edger)
1453 ("r-ggbio" ,r-ggbio)
1454 ("r-ggplot2" ,r-ggplot2)
1455 ("r-gostats" ,r-gostats)
1456 ("r-gseabase" ,r-gseabase)
1457 ("r-hwriter" ,r-hwriter)
1458 ("r-iranges" ,r-iranges)
1459 ("r-knitr" ,r-knitr)
1460 ("r-lattice" ,r-lattice)
1461 ("r-limma" ,r-limma)
1462 ("r-pfam-db" ,r-pfam-db)
1463 ("r-r-utils" ,r-r-utils)
1466 `(("r-knitr" ,r-knitr)))
1467 (home-page "https://bioconductor.org/packages/ReportingTools/")
1468 (synopsis "Tools for making reports in various formats")
1470 "The ReportingTools package enables users to easily display reports of
1471 analysis results generated from sources such as microarray and sequencing
1472 data. The package allows users to create HTML pages that may be viewed on a
1473 web browser, or in other formats. Users can generate tables with sortable and
1474 filterable columns, make and display plots, and link table entries to other
1475 data sources such as NCBI or larger plots within the HTML page. Using the
1476 package, users can also produce a table of contents page to link various
1477 reports together for a particular project that can be viewed in a web
1479 (license license:artistic2.0)))
1481 (define-public r-geneplotter
1483 (name "r-geneplotter")
1488 (uri (bioconductor-uri "geneplotter" version))
1491 "1y494da1llmrvn3qm7akwgwjazvpffabi8llw3fbday14cay1br5"))))
1492 (build-system r-build-system)
1494 `(("r-annotate" ,r-annotate)
1495 ("r-annotationdbi" ,r-annotationdbi)
1496 ("r-biobase" ,r-biobase)
1497 ("r-biocgenerics" ,r-biocgenerics)
1498 ("r-lattice" ,r-lattice)
1499 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1500 (home-page "https://bioconductor.org/packages/geneplotter")
1501 (synopsis "Graphics functions for genomic data")
1503 "This package provides functions for plotting genomic data.")
1504 (license license:artistic2.0)))
1506 (define-public r-oligoclasses
1508 (name "r-oligoclasses")
1513 (uri (bioconductor-uri "oligoClasses" version))
1516 "1d8c3i8v8kcm1afgpz6zc1iysip7993y8456cqxl37f7n6n0ax67"))))
1517 (properties `((upstream-name . "oligoClasses")))
1518 (build-system r-build-system)
1520 `(("r-affyio" ,r-affyio)
1521 ("r-biobase" ,r-biobase)
1522 ("r-biocgenerics" ,r-biocgenerics)
1523 ("r-biocmanager" ,r-biocmanager)
1524 ("r-biostrings" ,r-biostrings)
1527 ("r-foreach" ,r-foreach)
1528 ("r-genomicranges" ,r-genomicranges)
1529 ("r-iranges" ,r-iranges)
1530 ("r-rsqlite" ,r-rsqlite)
1531 ("r-s4vectors" ,r-s4vectors)
1532 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1533 (home-page "https://bioconductor.org/packages/oligoClasses/")
1534 (synopsis "Classes for high-throughput arrays")
1536 "This package contains class definitions, validity checks, and
1537 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1539 (license license:gpl2+)))
1541 (define-public r-oligo
1548 (uri (bioconductor-uri "oligo" version))
1551 "1gpvr33pwzz1glzajcipvjcplb7yxvjj00q0ybqcc3wa47bhfkwd"))))
1552 (properties `((upstream-name . "oligo")))
1553 (build-system r-build-system)
1554 (inputs `(("zlib" ,zlib)))
1556 `(("r-affxparser" ,r-affxparser)
1557 ("r-affyio" ,r-affyio)
1558 ("r-biobase" ,r-biobase)
1559 ("r-biocgenerics" ,r-biocgenerics)
1560 ("r-biostrings" ,r-biostrings)
1563 ("r-oligoclasses" ,r-oligoclasses)
1564 ("r-preprocesscore" ,r-preprocesscore)
1565 ("r-rsqlite" ,r-rsqlite)
1566 ("r-zlibbioc" ,r-zlibbioc)))
1568 `(("r-knitr" ,r-knitr)))
1569 (home-page "https://bioconductor.org/packages/oligo/")
1570 (synopsis "Preprocessing tools for oligonucleotide arrays")
1572 "This package provides a package to analyze oligonucleotide
1573 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1574 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1575 (license license:lgpl2.0+)))
1577 (define-public r-qvalue
1584 (uri (bioconductor-uri "qvalue" version))
1587 "1hndmdr9niagbr4ry0vbhffvjzjg9im27kdbn0sa774k6r5b4z3f"))))
1588 (build-system r-build-system)
1590 `(("r-ggplot2" ,r-ggplot2)
1591 ("r-reshape2" ,r-reshape2)))
1593 `(("r-knitr" ,r-knitr)))
1594 (home-page "https://github.com/StoreyLab/qvalue")
1595 (synopsis "Q-value estimation for false discovery rate control")
1597 "This package takes a list of p-values resulting from the simultaneous
1598 testing of many hypotheses and estimates their q-values and local @dfn{false
1599 discovery rate} (FDR) values. The q-value of a test measures the proportion
1600 of false positives incurred when that particular test is called significant.
1601 The local FDR measures the posterior probability the null hypothesis is true
1602 given the test's p-value. Various plots are automatically generated, allowing
1603 one to make sensible significance cut-offs. The software can be applied to
1604 problems in genomics, brain imaging, astrophysics, and data mining.")
1605 ;; Any version of the LGPL.
1606 (license license:lgpl3+)))
1608 (define-public r-diffbind
1615 (uri (bioconductor-uri "DiffBind" version))
1618 "1mwqgljya1c7r2dfrdds3nswn9bn1l3ak1wavbpv4lbv3nkmykn5"))))
1619 (properties `((upstream-name . "DiffBind")))
1620 (build-system r-build-system)
1624 `(("r-amap" ,r-amap)
1625 ("r-biocparallel" ,r-biocparallel)
1626 ("r-deseq2" ,r-deseq2)
1627 ("r-dplyr" ,r-dplyr)
1628 ("r-edger" ,r-edger)
1629 ("r-genomicalignments" ,r-genomicalignments)
1630 ("r-genomicranges" ,r-genomicranges)
1631 ("r-ggplot2" ,r-ggplot2)
1632 ("r-ggrepel" ,r-ggrepel)
1633 ("r-gplots" ,r-gplots)
1634 ("r-iranges" ,r-iranges)
1635 ("r-lattice" ,r-lattice)
1636 ("r-limma" ,r-limma)
1637 ("r-locfit" ,r-locfit)
1638 ("r-rcolorbrewer" , r-rcolorbrewer)
1640 ("r-rhtslib" ,r-rhtslib)
1641 ("r-rsamtools" ,r-rsamtools)
1642 ("r-s4vectors" ,r-s4vectors)
1643 ("r-summarizedexperiment" ,r-summarizedexperiment)
1644 ("r-systempiper" ,r-systempiper)))
1645 (home-page "https://bioconductor.org/packages/DiffBind")
1646 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1648 "This package computes differentially bound sites from multiple
1649 ChIP-seq experiments using affinity (quantitative) data. Also enables
1650 occupancy (overlap) analysis and plotting functions.")
1651 (license license:artistic2.0)))
1653 (define-public r-ripseeker
1655 (name "r-ripseeker")
1660 (uri (bioconductor-uri "RIPSeeker" version))
1663 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
1664 (properties `((upstream-name . "RIPSeeker")))
1665 (build-system r-build-system)
1667 `(("r-s4vectors" ,r-s4vectors)
1668 ("r-iranges" ,r-iranges)
1669 ("r-genomicranges" ,r-genomicranges)
1670 ("r-summarizedexperiment" ,r-summarizedexperiment)
1671 ("r-rsamtools" ,r-rsamtools)
1672 ("r-genomicalignments" ,r-genomicalignments)
1673 ("r-rtracklayer" ,r-rtracklayer)))
1674 (home-page "https://bioconductor.org/packages/RIPSeeker")
1676 "Identifying protein-associated transcripts from RIP-seq experiments")
1678 "This package infers and discriminates RIP peaks from RIP-seq alignments
1679 using two-state HMM with negative binomial emission probability. While
1680 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1681 a suite of bioinformatics tools integrated within this self-contained software
1682 package comprehensively addressing issues ranging from post-alignments
1683 processing to visualization and annotation.")
1684 (license license:gpl2)))
1686 (define-public r-multtest
1693 (uri (bioconductor-uri "multtest" version))
1696 "12li7nzzygm3sjfx472095irqpawixk48d0k591wlnrms6sxchx2"))))
1697 (build-system r-build-system)
1699 `(("r-survival" ,r-survival)
1700 ("r-biocgenerics" ,r-biocgenerics)
1701 ("r-biobase" ,r-biobase)
1702 ("r-mass" ,r-mass)))
1703 (home-page "https://bioconductor.org/packages/multtest")
1704 (synopsis "Resampling-based multiple hypothesis testing")
1706 "This package can do non-parametric bootstrap and permutation
1707 resampling-based multiple testing procedures (including empirical Bayes
1708 methods) for controlling the family-wise error rate (FWER), generalized
1709 family-wise error rate (gFWER), tail probability of the proportion of
1710 false positives (TPPFP), and false discovery rate (FDR). Several choices
1711 of bootstrap-based null distribution are implemented (centered, centered
1712 and scaled, quantile-transformed). Single-step and step-wise methods are
1713 available. Tests based on a variety of T- and F-statistics (including
1714 T-statistics based on regression parameters from linear and survival models
1715 as well as those based on correlation parameters) are included. When probing
1716 hypotheses with T-statistics, users may also select a potentially faster null
1717 distribution which is multivariate normal with mean zero and variance
1718 covariance matrix derived from the vector influence function. Results are
1719 reported in terms of adjusted P-values, confidence regions and test statistic
1720 cutoffs. The procedures are directly applicable to identifying differentially
1721 expressed genes in DNA microarray experiments.")
1722 (license license:lgpl3)))
1724 (define-public r-graph
1730 (uri (bioconductor-uri "graph" version))
1733 "15v0nx9gzpszmdn5lil1s1y8qfmsirlznh56wcyqq4sxwjbyjn9g"))))
1734 (build-system r-build-system)
1736 `(("r-biocgenerics" ,r-biocgenerics)))
1737 (home-page "https://bioconductor.org/packages/graph")
1738 (synopsis "Handle graph data structures in R")
1740 "This package implements some simple graph handling capabilities for R.")
1741 (license license:artistic2.0)))
1743 ;; This is a CRAN package, but it depends on a Bioconductor package.
1744 (define-public r-ggm
1751 (uri (cran-uri "ggm" version))
1754 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
1755 (properties `((upstream-name . "ggm")))
1756 (build-system r-build-system)
1758 `(("r-graph" ,r-graph)
1759 ("r-igraph" ,r-igraph)))
1760 (home-page "https://cran.r-project.org/package=ggm")
1761 (synopsis "Functions for graphical Markov models")
1763 "This package provides functions and datasets for maximum likelihood
1764 fitting of some classes of graphical Markov models.")
1765 (license license:gpl2+)))
1767 ;; This is a CRAN package, but it depends on a Bioconductor package.
1768 (define-public r-codedepends
1770 (name "r-codedepends")
1775 (uri (cran-uri "CodeDepends" version))
1778 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1779 (properties `((upstream-name . "CodeDepends")))
1780 (build-system r-build-system)
1782 `(("r-codetools" ,r-codetools)
1783 ("r-graph" ,r-graph)
1785 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
1786 (synopsis "Analysis of R code for reproducible research and code comprehension")
1788 "This package provides tools for analyzing R expressions or blocks of
1789 code and determining the dependencies between them. It focuses on R scripts,
1790 but can be used on the bodies of functions. There are many facilities
1791 including the ability to summarize or get a high-level view of code,
1792 determining dependencies between variables, code improvement suggestions.")
1793 ;; Any version of the GPL
1794 (license (list license:gpl2+ license:gpl3+))))
1796 (define-public r-chippeakanno
1798 (name "r-chippeakanno")
1803 (uri (bioconductor-uri "ChIPpeakAnno" version))
1806 "0q3f55hh0a2hl96272js6gagmgps9cxs8s13pf6fii64rzaz5m7y"))))
1807 (properties `((upstream-name . "ChIPpeakAnno")))
1808 (build-system r-build-system)
1810 `(("r-annotationdbi" ,r-annotationdbi)
1811 ("r-biobase" ,r-biobase)
1812 ("r-biocgenerics" ,r-biocgenerics)
1813 ("r-biocmanager" ,r-biocmanager)
1814 ("r-biomart" ,r-biomart)
1815 ("r-biostrings" ,r-biostrings)
1816 ("r-bsgenome" ,r-bsgenome)
1818 ("r-delayedarray" ,r-delayedarray)
1819 ("r-ensembldb" ,r-ensembldb)
1820 ("r-genomeinfodb" ,r-genomeinfodb)
1821 ("r-genomicalignments" ,r-genomicalignments)
1822 ("r-genomicfeatures" ,r-genomicfeatures)
1823 ("r-genomicranges" ,r-genomicranges)
1824 ("r-go-db" ,r-go-db)
1825 ("r-graph" ,r-graph)
1827 ("r-iranges" ,r-iranges)
1828 ("r-limma" ,r-limma)
1829 ("r-matrixstats" ,r-matrixstats)
1830 ("r-multtest" ,r-multtest)
1832 ("r-regioner" ,r-regioner)
1833 ("r-rsamtools" ,r-rsamtools)
1834 ("r-rtracklayer" ,r-rtracklayer)
1835 ("r-s4vectors" ,r-s4vectors)
1836 ("r-seqinr" ,r-seqinr)
1837 ("r-summarizedexperiment" ,r-summarizedexperiment)
1838 ("r-venndiagram" ,r-venndiagram)))
1840 `(("r-knitr" ,r-knitr)))
1841 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
1842 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1844 "The package includes functions to retrieve the sequences around the peak,
1845 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1846 custom features such as most conserved elements and other transcription factor
1847 binding sites supplied by users. Starting 2.0.5, new functions have been added
1848 for finding the peaks with bi-directional promoters with summary statistics
1849 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1850 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1851 enrichedGO (addGeneIDs).")
1852 (license license:gpl2+)))
1854 (define-public r-marray
1860 (uri (bioconductor-uri "marray" version))
1862 (base32 "1sym3nis5qzg05b2in83xr019mvz8czy8qvispc0hzsq42yng6kd"))))
1863 (build-system r-build-system)
1865 `(("r-limma" ,r-limma)))
1866 (home-page "https://bioconductor.org/packages/marray")
1867 (synopsis "Exploratory analysis for two-color spotted microarray data")
1868 (description "This package contains class definitions for two-color spotted
1869 microarray data. It also includes functions for data input, diagnostic plots,
1870 normalization and quality checking.")
1871 (license license:lgpl2.0+)))
1873 (define-public r-cghbase
1879 (uri (bioconductor-uri "CGHbase" version))
1881 (base32 "0gfqqa9rs5hid53ihlky88qndgrwxxz0s6j7s505f660dd5nzlkf"))))
1882 (properties `((upstream-name . "CGHbase")))
1883 (build-system r-build-system)
1885 `(("r-biobase" ,r-biobase)
1886 ("r-marray" ,r-marray)))
1887 (home-page "https://bioconductor.org/packages/CGHbase")
1888 (synopsis "Base functions and classes for arrayCGH data analysis")
1889 (description "This package contains functions and classes that are needed by
1890 the @code{arrayCGH} packages.")
1891 (license license:gpl2+)))
1893 (define-public r-cghcall
1899 (uri (bioconductor-uri "CGHcall" version))
1901 (base32 "1dz6sag8khl18vkb97b5w6fk6k9s7s9xxnc467dd3bmhmajlmrrg"))))
1902 (properties `((upstream-name . "CGHcall")))
1903 (build-system r-build-system)
1905 `(("r-biobase" ,r-biobase)
1906 ("r-cghbase" ,r-cghbase)
1907 ("r-impute" ,r-impute)
1908 ("r-dnacopy" ,r-dnacopy)
1909 ("r-snowfall" ,r-snowfall)))
1910 (home-page "https://bioconductor.org/packages/CGHcall")
1911 (synopsis "Base functions and classes for arrayCGH data analysis")
1912 (description "This package contains functions and classes that are needed by
1913 @code{arrayCGH} packages.")
1914 (license license:gpl2+)))
1916 (define-public r-qdnaseq
1922 (uri (bioconductor-uri "QDNAseq" version))
1924 (base32 "1ji9pl2r1idyj3qzggj7qd2kqx31i6b3igwk2hqjb8qzkyb37p86"))))
1925 (properties `((upstream-name . "QDNAseq")))
1926 (build-system r-build-system)
1928 `(("r-biobase" ,r-biobase)
1929 ("r-cghbase" ,r-cghbase)
1930 ("r-cghcall" ,r-cghcall)
1931 ("r-dnacopy" ,r-dnacopy)
1932 ("r-future" ,r-future)
1933 ("r-future-apply" ,r-future-apply)
1934 ("r-genomicranges" ,r-genomicranges)
1935 ("r-iranges" ,r-iranges)
1936 ("r-matrixstats" ,r-matrixstats)
1937 ("r-r-utils" ,r-r-utils)
1938 ("r-rsamtools" ,r-rsamtools)))
1939 (home-page "https://bioconductor.org/packages/QDNAseq")
1940 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1941 (description "The genome is divided into non-overlapping fixed-sized bins,
1942 number of sequence reads in each counted, adjusted with a simultaneous
1943 two-dimensional loess correction for sequence mappability and GC content, and
1944 filtered to remove spurious regions in the genome. Downstream steps of
1945 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1947 (license license:gpl2+)))
1949 (define-public r-bayseq
1956 (uri (bioconductor-uri "baySeq" version))
1959 "1x0d34pqv9s15nmmxsfbw0ycxbf5348mi30ahycarjkjsyzycymj"))))
1960 (properties `((upstream-name . "baySeq")))
1961 (build-system r-build-system)
1963 `(("r-abind" ,r-abind)
1964 ("r-edger" ,r-edger)
1965 ("r-genomicranges" ,r-genomicranges)))
1966 (home-page "https://bioconductor.org/packages/baySeq/")
1967 (synopsis "Bayesian analysis of differential expression patterns in count data")
1969 "This package identifies differential expression in high-throughput count
1970 data, such as that derived from next-generation sequencing machines,
1971 calculating estimated posterior likelihoods of differential expression (or
1972 more complex hypotheses) via empirical Bayesian methods.")
1973 (license license:gpl3)))
1975 (define-public r-chipcomp
1982 (uri (bioconductor-uri "ChIPComp" version))
1985 "0780kj9vbzdhf2jkfb1my8m58pcdwk6jqw6zfng82g46jias98cp"))))
1986 (properties `((upstream-name . "ChIPComp")))
1987 (build-system r-build-system)
1989 `(("r-biocgenerics" ,r-biocgenerics)
1990 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1991 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1992 ("r-genomeinfodb" ,r-genomeinfodb)
1993 ("r-genomicranges" ,r-genomicranges)
1994 ("r-iranges" ,r-iranges)
1995 ("r-limma" ,r-limma)
1996 ("r-rsamtools" ,r-rsamtools)
1997 ("r-rtracklayer" ,r-rtracklayer)
1998 ("r-s4vectors" ,r-s4vectors)))
1999 (home-page "https://bioconductor.org/packages/ChIPComp")
2000 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
2002 "ChIPComp implements a statistical method for quantitative comparison of
2003 multiple ChIP-seq datasets. It detects differentially bound sharp binding
2004 sites across multiple conditions considering matching control in ChIP-seq
2006 ;; Any version of the GPL.
2007 (license license:gpl3+)))
2009 (define-public r-riboprofiling
2011 (name "r-riboprofiling")
2016 (uri (bioconductor-uri "RiboProfiling" version))
2019 "0s30m96dbbrzbywz3wai5ar0nsshb16lq101nyl20w1bk7sk2bha"))))
2020 (properties `((upstream-name . "RiboProfiling")))
2021 (build-system r-build-system)
2023 `(("r-biocgenerics" ,r-biocgenerics)
2024 ("r-biostrings" ,r-biostrings)
2025 ("r-data-table" ,r-data-table)
2026 ("r-genomeinfodb" ,r-genomeinfodb)
2027 ("r-genomicalignments" ,r-genomicalignments)
2028 ("r-genomicfeatures" ,r-genomicfeatures)
2029 ("r-genomicranges" ,r-genomicranges)
2030 ("r-ggbio" ,r-ggbio)
2031 ("r-ggplot2" ,r-ggplot2)
2032 ("r-iranges" ,r-iranges)
2034 ("r-reshape2" ,r-reshape2)
2035 ("r-rsamtools" ,r-rsamtools)
2036 ("r-rtracklayer" ,r-rtracklayer)
2037 ("r-s4vectors" ,r-s4vectors)
2038 ("r-sqldf" ,r-sqldf)))
2040 `(("r-knitr" ,r-knitr)))
2041 (home-page "https://bioconductor.org/packages/RiboProfiling/")
2042 (synopsis "Ribosome profiling data analysis")
2043 (description "Starting with a BAM file, this package provides the
2044 necessary functions for quality assessment, read start position recalibration,
2045 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
2046 of count data: pairs, log fold-change, codon frequency and coverage
2047 assessment, principal component analysis on codon coverage.")
2048 (license license:gpl3)))
2050 (define-public r-riboseqr
2057 (uri (bioconductor-uri "riboSeqR" version))
2060 "04a4dkmacd6xy55m84amxa0fspbc4kgg9r9k7bc3wrxswk77ccxk"))))
2061 (properties `((upstream-name . "riboSeqR")))
2062 (build-system r-build-system)
2064 `(("r-abind" ,r-abind)
2065 ("r-bayseq" ,r-bayseq)
2066 ("r-genomeinfodb" ,r-genomeinfodb)
2067 ("r-genomicranges" ,r-genomicranges)
2068 ("r-iranges" ,r-iranges)
2069 ("r-rsamtools" ,r-rsamtools)
2070 ("r-seqlogo" ,r-seqlogo)))
2071 (home-page "https://bioconductor.org/packages/riboSeqR/")
2072 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
2074 "This package provides plotting functions, frameshift detection and
2075 parsing of genetic sequencing data from ribosome profiling experiments.")
2076 (license license:gpl3)))
2078 (define-public r-interactionset
2080 (name "r-interactionset")
2085 (uri (bioconductor-uri "InteractionSet" version))
2088 "1nsivm9j0mzkfhwqsa2y9gxxdbaplg4z8vn5dfvls3nrihnqpk4v"))))
2090 `((upstream-name . "InteractionSet")))
2091 (build-system r-build-system)
2093 `(("r-biocgenerics" ,r-biocgenerics)
2094 ("r-genomeinfodb" ,r-genomeinfodb)
2095 ("r-genomicranges" ,r-genomicranges)
2096 ("r-iranges" ,r-iranges)
2097 ("r-matrix" ,r-matrix)
2099 ("r-s4vectors" ,r-s4vectors)
2100 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2102 `(("r-knitr" ,r-knitr)))
2103 (home-page "https://bioconductor.org/packages/InteractionSet")
2104 (synopsis "Base classes for storing genomic interaction data")
2106 "This package provides the @code{GInteractions},
2107 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
2108 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
2110 (license license:gpl3)))
2112 (define-public r-genomicinteractions
2114 (name "r-genomicinteractions")
2119 (uri (bioconductor-uri "GenomicInteractions" version))
2122 "0fg66v31nfajb40da6gxpigm2z11ywkdijs7npvc1mr62ynx9qmy"))))
2124 `((upstream-name . "GenomicInteractions")))
2125 (build-system r-build-system)
2127 `(("r-biobase" ,r-biobase)
2128 ("r-biocgenerics" ,r-biocgenerics)
2129 ("r-data-table" ,r-data-table)
2130 ("r-dplyr" ,r-dplyr)
2131 ("r-genomeinfodb" ,r-genomeinfodb)
2132 ("r-genomicranges" ,r-genomicranges)
2133 ("r-ggplot2" ,r-ggplot2)
2134 ("r-gridextra" ,r-gridextra)
2136 ("r-igraph" ,r-igraph)
2137 ("r-interactionset" ,r-interactionset)
2138 ("r-iranges" ,r-iranges)
2139 ("r-rsamtools" ,r-rsamtools)
2140 ("r-rtracklayer" ,r-rtracklayer)
2141 ("r-s4vectors" ,r-s4vectors)
2142 ("r-stringr" ,r-stringr)))
2144 `(("r-knitr" ,r-knitr)))
2145 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
2146 (synopsis "R package for handling genomic interaction data")
2148 "This R package provides tools for handling genomic interaction data,
2149 such as ChIA-PET/Hi-C, annotating genomic features with interaction
2150 information and producing various plots and statistics.")
2151 (license license:gpl3)))
2153 (define-public r-ctc
2160 (uri (bioconductor-uri "ctc" version))
2163 "0lv126xj092hps3f3dsv7hasdyy26wcx8npl9idq2l4h9addk6v6"))))
2164 (build-system r-build-system)
2165 (propagated-inputs `(("r-amap" ,r-amap)))
2166 (home-page "https://bioconductor.org/packages/ctc/")
2167 (synopsis "Cluster and tree conversion")
2169 "This package provides tools for exporting and importing classification
2170 trees and clusters to other programs.")
2171 (license license:gpl2)))
2173 (define-public r-goseq
2180 (uri (bioconductor-uri "goseq" version))
2183 "1iyri4rrchzsn8p6wjxr4k30d3cqx3km5mnd9hkfm5d0s7fjzlym"))))
2184 (build-system r-build-system)
2186 `(("r-annotationdbi" ,r-annotationdbi)
2187 ("r-biasedurn" ,r-biasedurn)
2188 ("r-biocgenerics" ,r-biocgenerics)
2189 ("r-genelendatabase" ,r-genelendatabase)
2190 ("r-go-db" ,r-go-db)
2191 ("r-mgcv" ,r-mgcv)))
2192 (home-page "https://bioconductor.org/packages/goseq/")
2193 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
2195 "This package provides tools to detect Gene Ontology and/or other user
2196 defined categories which are over/under represented in RNA-seq data.")
2197 (license license:lgpl2.0+)))
2199 (define-public r-glimma
2206 (uri (bioconductor-uri "Glimma" version))
2209 "1bxfgwjqb9p400a5a5q6p17kcnl3ddz090llihkfih9kyxii9n4y"))))
2210 (properties `((upstream-name . "Glimma")))
2211 (build-system r-build-system)
2213 `(("r-edger" ,r-edger)
2214 ("r-jsonlite" ,r-jsonlite)
2215 ("r-s4vectors" ,r-s4vectors)))
2217 `(("r-knitr" ,r-knitr)))
2218 (home-page "https://github.com/Shians/Glimma")
2219 (synopsis "Interactive HTML graphics")
2221 "This package generates interactive visualisations for analysis of
2222 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2223 HTML page. The interactions are built on top of the popular static
2224 representations of analysis results in order to provide additional
2226 (license license:lgpl3)))
2228 (define-public r-rots
2235 (uri (bioconductor-uri "ROTS" version))
2238 "1mqhi1rfiw7mhiyify7vm3w17p7sc76wjda3ak6690hrc3gsm3cm"))))
2239 (properties `((upstream-name . "ROTS")))
2240 (build-system r-build-system)
2242 `(("r-biobase" ,r-biobase)
2243 ("r-rcpp" ,r-rcpp)))
2244 (home-page "https://bioconductor.org/packages/ROTS/")
2245 (synopsis "Reproducibility-Optimized Test Statistic")
2247 "This package provides tools for calculating the
2248 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2250 (license license:gpl2+)))
2252 (define-public r-plgem
2259 (uri (bioconductor-uri "plgem" version))
2262 "1fs5nbjnrm7x23y7d9krq56r1kzxka40ca1rs6sq70mn6syhj90a"))))
2263 (build-system r-build-system)
2265 `(("r-biobase" ,r-biobase)
2266 ("r-mass" ,r-mass)))
2267 (home-page "http://www.genopolis.it")
2268 (synopsis "Detect differential expression in microarray and proteomics datasets")
2270 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2271 model the variance-versus-mean dependence that exists in a variety of
2272 genome-wide datasets, including microarray and proteomics data. The use of
2273 PLGEM has been shown to improve the detection of differentially expressed
2274 genes or proteins in these datasets.")
2275 (license license:gpl2)))
2277 (define-public r-inspect
2284 (uri (bioconductor-uri "INSPEcT" version))
2287 "1yyglkdc3ww2jzswhcxk9g1imydfm39krl87as5l9fbm7mv3vd4z"))))
2288 (properties `((upstream-name . "INSPEcT")))
2289 (build-system r-build-system)
2291 `(("r-biobase" ,r-biobase)
2292 ("r-biocgenerics" ,r-biocgenerics)
2293 ("r-biocparallel" ,r-biocparallel)
2294 ("r-deseq2" ,r-deseq2)
2295 ("r-desolve" ,r-desolve)
2296 ("r-gdata" ,r-gdata)
2297 ("r-genomeinfodb" ,r-genomeinfodb)
2298 ("r-genomicalignments" ,r-genomicalignments)
2299 ("r-genomicfeatures" ,r-genomicfeatures)
2300 ("r-genomicranges" ,r-genomicranges)
2301 ("r-iranges" ,r-iranges)
2302 ("r-kernsmooth" ,r-kernsmooth)
2303 ("r-plgem" ,r-plgem)
2305 ("r-rootsolve" ,r-rootsolve)
2306 ("r-rsamtools" ,r-rsamtools)
2307 ("r-rtracklayer" ,r-rtracklayer)
2308 ("r-s4vectors" ,r-s4vectors)
2309 ("r-shiny" ,r-shiny)
2310 ("r-summarizedexperiment" ,r-summarizedexperiment)
2311 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2312 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2314 `(("r-knitr" ,r-knitr)))
2315 (home-page "https://bioconductor.org/packages/INSPEcT")
2316 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2318 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2319 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2320 order to evaluate synthesis, processing and degradation rates and assess via
2321 modeling the rates that determines changes in mature mRNA levels.")
2322 (license license:gpl2)))
2324 (define-public r-dnabarcodes
2326 (name "r-dnabarcodes")
2331 (uri (bioconductor-uri "DNABarcodes" version))
2334 "03y39hjpkb05fnawy3k797bph1iydi1blmpgyy4244zjgk6rs5x7"))))
2335 (properties `((upstream-name . "DNABarcodes")))
2336 (build-system r-build-system)
2339 ("r-matrix" ,r-matrix)
2340 ("r-rcpp" ,r-rcpp)))
2342 `(("r-knitr" ,r-knitr)))
2343 (home-page "https://bioconductor.org/packages/DNABarcodes")
2344 (synopsis "Create and analyze DNA barcodes")
2346 "This package offers tools to create DNA barcode sets capable of
2347 correcting insertion, deletion, and substitution errors. Existing barcodes
2348 can be analyzed regarding their minimal, maximal and average distances between
2349 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2350 demultiplexed, i.e. assigned to their original reference barcode.")
2351 (license license:gpl2)))
2353 (define-public r-ruvseq
2360 (uri (bioconductor-uri "RUVSeq" version))
2363 "0yqs9xgyzw3cwb4l7zjl1cjgbsjp05qrqnwyvh7q81wdp7x5p55x"))))
2364 (properties `((upstream-name . "RUVSeq")))
2365 (build-system r-build-system)
2367 `(("r-biobase" ,r-biobase)
2368 ("r-edaseq" ,r-edaseq)
2369 ("r-edger" ,r-edger)
2370 ("r-mass" ,r-mass)))
2372 `(("r-knitr" ,r-knitr)))
2373 (home-page "https://github.com/drisso/RUVSeq")
2374 (synopsis "Remove unwanted variation from RNA-Seq data")
2376 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2377 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2379 (license license:artistic2.0)))
2381 (define-public r-biocneighbors
2383 (name "r-biocneighbors")
2388 (uri (bioconductor-uri "BiocNeighbors" version))
2391 "14cyyrwxi82xm5wy6bb1176zg322ll67wjrw9vvi4fhfs1k4wqxy"))))
2392 (properties `((upstream-name . "BiocNeighbors")))
2393 (build-system r-build-system)
2395 `(("r-biocparallel" ,r-biocparallel)
2396 ("r-matrix" ,r-matrix)
2398 ("r-rcppannoy" ,r-rcppannoy)
2399 ("r-rcpphnsw" ,r-rcpphnsw)
2400 ("r-s4vectors" ,r-s4vectors)))
2402 `(("r-knitr" ,r-knitr)))
2403 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2404 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2406 "This package implements exact and approximate methods for nearest
2407 neighbor detection, in a framework that allows them to be easily switched
2408 within Bioconductor packages or workflows. The exact algorithm is implemented
2409 using pre-clustering with the k-means algorithm. Functions are also provided
2410 to search for all neighbors within a given distance. Parallelization is
2411 achieved for all methods using the BiocParallel framework.")
2412 (license license:gpl3)))
2414 (define-public r-biocsingular
2416 (name "r-biocsingular")
2421 (uri (bioconductor-uri "BiocSingular" version))
2424 "0368a9xj4cvicqkxmhh12ln46q9gnxla70s1dqrxxfn3b6k525ih"))))
2425 (properties `((upstream-name . "BiocSingular")))
2426 (build-system r-build-system)
2428 `(("r-beachmat" ,r-beachmat)
2429 ("r-biocgenerics" ,r-biocgenerics)
2430 ("r-biocparallel" ,r-biocparallel)
2431 ("r-delayedarray" ,r-delayedarray)
2432 ("r-irlba" ,r-irlba)
2433 ("r-matrix" ,r-matrix)
2436 ("r-s4vectors" ,r-s4vectors)))
2438 `(("r-knitr" ,r-knitr)))
2439 (home-page "https://github.com/LTLA/BiocSingular")
2440 (synopsis "Singular value decomposition for Bioconductor packages")
2442 "This package implements exact and approximate methods for singular value
2443 decomposition and principal components analysis, in a framework that allows
2444 them to be easily switched within Bioconductor packages or workflows. Where
2445 possible, parallelization is achieved using the BiocParallel framework.")
2446 (license license:gpl3)))
2448 (define-public r-destiny
2455 (uri (bioconductor-uri "destiny" version))
2458 "0ik5vwxz9cci3glwgb5ff03sfyr4sjcp8ckfymlgmlm6fz8cp21n"))))
2459 (build-system r-build-system)
2461 `(("r-biobase" ,r-biobase)
2462 ("r-biocgenerics" ,r-biocgenerics)
2463 ("r-ggplot-multistats" ,r-ggplot-multistats)
2464 ("r-ggplot2" ,r-ggplot2)
2465 ("r-ggthemes" ,r-ggthemes)
2466 ("r-irlba" ,r-irlba)
2467 ("r-knn-covertree" ,r-knn-covertree)
2468 ("r-matrix" ,r-matrix)
2469 ("r-nbconvertr" ,r-nbconvertr)
2470 ("r-pcamethods" ,r-pcamethods)
2471 ("r-proxy" ,r-proxy)
2473 ("r-rcppeigen" ,r-rcppeigen)
2474 ("r-rcpphnsw" ,r-rcpphnsw)
2475 ("r-rspectra" ,r-rspectra)
2476 ("r-scales" ,r-scales)
2477 ("r-scatterplot3d" ,r-scatterplot3d)
2478 ("r-singlecellexperiment" ,r-singlecellexperiment)
2479 ("r-smoother" ,r-smoother)
2480 ("r-summarizedexperiment" ,r-summarizedexperiment)
2481 ("r-tidyr" ,r-tidyr)
2482 ("r-tidyselect" ,r-tidyselect)
2485 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
2486 (home-page "https://bioconductor.org/packages/destiny/")
2487 (synopsis "Create and plot diffusion maps")
2488 (description "This package provides tools to create and plot diffusion
2490 ;; Any version of the GPL
2491 (license license:gpl3+)))
2493 (define-public r-savr
2500 (uri (bioconductor-uri "savR" version))
2503 "17jdnr47ivblfspr4b32z9fds1fqiiwsi2z6r524g1v4944p8w5a"))))
2504 (properties `((upstream-name . "savR")))
2505 (build-system r-build-system)
2507 `(("r-ggplot2" ,r-ggplot2)
2508 ("r-gridextra" ,r-gridextra)
2509 ("r-reshape2" ,r-reshape2)
2510 ("r-scales" ,r-scales)
2512 (home-page "https://github.com/bcalder/savR")
2513 (synopsis "Parse and analyze Illumina SAV files")
2515 "This package provides tools to parse Illumina Sequence Analysis
2516 Viewer (SAV) files, access data, and generate QC plots.")
2517 (license license:agpl3+)))
2519 (define-public r-chipexoqual
2521 (name "r-chipexoqual")
2526 (uri (bioconductor-uri "ChIPexoQual" version))
2529 "02rsf1rvm0p6dn18zq2a4hpvpd9m2i5rziyi4zm8j43qvs8xhafp"))))
2530 (properties `((upstream-name . "ChIPexoQual")))
2531 (build-system r-build-system)
2533 `(("r-biocparallel" ,r-biocparallel)
2534 ("r-biovizbase" ,r-biovizbase)
2535 ("r-broom" ,r-broom)
2536 ("r-data-table" ,r-data-table)
2537 ("r-dplyr" ,r-dplyr)
2538 ("r-genomeinfodb" ,r-genomeinfodb)
2539 ("r-genomicalignments" ,r-genomicalignments)
2540 ("r-genomicranges" ,r-genomicranges)
2541 ("r-ggplot2" ,r-ggplot2)
2542 ("r-hexbin" ,r-hexbin)
2543 ("r-iranges" ,r-iranges)
2544 ("r-rcolorbrewer" ,r-rcolorbrewer)
2545 ("r-rmarkdown" ,r-rmarkdown)
2546 ("r-rsamtools" ,r-rsamtools)
2547 ("r-s4vectors" ,r-s4vectors)
2548 ("r-scales" ,r-scales)
2549 ("r-viridis" ,r-viridis)))
2551 `(("r-knitr" ,r-knitr)))
2552 (home-page "https://github.com/keleslab/ChIPexoQual")
2553 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2555 "This package provides a quality control pipeline for ChIP-exo/nexus
2557 (license license:gpl2+)))
2559 (define-public r-copynumber
2561 (name "r-copynumber")
2565 (uri (bioconductor-uri "copynumber" version))
2568 "1b7v6xijpi2mir49cf83gpadhxm5pnbs6d8q8qga7y06hn9jx6my"))))
2569 (build-system r-build-system)
2571 `(("r-s4vectors" ,r-s4vectors)
2572 ("r-iranges" ,r-iranges)
2573 ("r-genomicranges" ,r-genomicranges)
2574 ("r-biocgenerics" ,r-biocgenerics)))
2575 (home-page "https://bioconductor.org/packages/copynumber")
2576 (synopsis "Segmentation of single- and multi-track copy number data")
2578 "This package segments single- and multi-track copy number data by a
2579 penalized least squares regression method.")
2580 (license license:artistic2.0)))
2582 (define-public r-dnacopy
2589 (uri (bioconductor-uri "DNAcopy" version))
2592 "0jg8lr83drzfs5h73c7mk7x99vj99a2p2s1sqjc4gicn927xvhza"))))
2593 (properties `((upstream-name . "DNAcopy")))
2594 (build-system r-build-system)
2595 (native-inputs `(("gfortran" ,gfortran)))
2596 (home-page "https://bioconductor.org/packages/DNAcopy")
2597 (synopsis "DNA copy number data analysis")
2599 "This package implements the @dfn{circular binary segmentation} (CBS)
2600 algorithm to segment DNA copy number data and identify genomic regions with
2601 abnormal copy number.")
2602 (license license:gpl2+)))
2604 ;; This is a CRAN package, but it uncharacteristically depends on a
2605 ;; Bioconductor package.
2606 (define-public r-htscluster
2608 (name "r-htscluster")
2613 (uri (cran-uri "HTSCluster" version))
2616 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2617 (properties `((upstream-name . "HTSCluster")))
2618 (build-system r-build-system)
2620 `(("r-capushe" ,r-capushe)
2621 ("r-edger" ,r-edger)
2622 ("r-plotrix" ,r-plotrix)))
2623 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2624 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2626 "This package provides a Poisson mixture model is implemented to cluster
2627 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2628 estimation is performed using either the EM or CEM algorithm, and the slope
2629 heuristics are used for model selection (i.e., to choose the number of
2631 (license license:gpl3+)))
2633 (define-public r-deds
2640 (uri (bioconductor-uri "DEDS" version))
2643 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
2644 (properties `((upstream-name . "DEDS")))
2645 (build-system r-build-system)
2646 (home-page "https://bioconductor.org/packages/DEDS/")
2647 (synopsis "Differential expression via distance summary for microarray data")
2649 "This library contains functions that calculate various statistics of
2650 differential expression for microarray data, including t statistics, fold
2651 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2652 also implements a new methodology called DEDS (Differential Expression via
2653 Distance Summary), which selects differentially expressed genes by integrating
2654 and summarizing a set of statistics using a weighted distance approach.")
2655 ;; Any version of the LGPL.
2656 (license license:lgpl3+)))
2658 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2660 (define-public r-nbpseq
2667 (uri (cran-uri "NBPSeq" version))
2670 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2671 (properties `((upstream-name . "NBPSeq")))
2672 (build-system r-build-system)
2674 `(("r-qvalue" ,r-qvalue)))
2675 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2676 (synopsis "Negative binomial models for RNA-Seq data")
2678 "This package provides negative binomial models for two-group comparisons
2679 and regression inferences from RNA-sequencing data.")
2680 (license license:gpl2)))
2682 (define-public r-ebseq
2689 (uri (bioconductor-uri "EBSeq" version))
2692 "0s9r1xxpfm5794ipjm5a5c8gfxicc6arma6f74aaz8zi5y5q9x5f"))))
2693 (properties `((upstream-name . "EBSeq")))
2694 (build-system r-build-system)
2696 `(("r-blockmodeling" ,r-blockmodeling)
2697 ("r-gplots" ,r-gplots)
2698 ("r-testthat" ,r-testthat)))
2699 (home-page "https://bioconductor.org/packages/EBSeq")
2700 (synopsis "Differential expression analysis of RNA-seq data")
2702 "This package provides tools for differential expression analysis at both
2703 gene and isoform level using RNA-seq data")
2704 (license license:artistic2.0)))
2706 (define-public r-karyoploter
2708 (name "r-karyoploter")
2712 (uri (bioconductor-uri "karyoploteR" version))
2715 "0h0gk4xd95k5phy6qcsv7j931d7gk3p24i2fg4mz5dsk110lpifs"))))
2716 (build-system r-build-system)
2718 `(("r-annotationdbi" ,r-annotationdbi)
2719 ("r-bamsignals" ,r-bamsignals)
2720 ("r-bezier" ,r-bezier)
2721 ("r-biovizbase" ,r-biovizbase)
2722 ("r-digest" ,r-digest)
2723 ("r-genomeinfodb" ,r-genomeinfodb)
2724 ("r-genomicfeatures" ,r-genomicfeatures)
2725 ("r-genomicranges" ,r-genomicranges)
2726 ("r-iranges" ,r-iranges)
2727 ("r-memoise" ,r-memoise)
2728 ("r-regioner" ,r-regioner)
2729 ("r-rsamtools" ,r-rsamtools)
2730 ("r-rtracklayer" ,r-rtracklayer)
2731 ("r-s4vectors" ,r-s4vectors)
2732 ("r-variantannotation" ,r-variantannotation)))
2734 `(("r-knitr" ,r-knitr)))
2735 (home-page "https://bioconductor.org/packages/karyoploteR/")
2736 (synopsis "Plot customizable linear genomes displaying arbitrary data")
2737 (description "This package creates karyotype plots of arbitrary genomes and
2738 offers a complete set of functions to plot arbitrary data on them. It mimicks
2739 many R base graphics functions coupling them with a coordinate change function
2740 automatically mapping the chromosome and data coordinates into the plot
2742 (license license:artistic2.0)))
2744 (define-public r-lpsymphony
2746 (name "r-lpsymphony")
2751 (uri (bioconductor-uri "lpsymphony" version))
2754 "072ikmd267n18hrj7dip4dp1vb5dinj82p3h95n2jaf04h9hwfn4"))))
2755 (build-system r-build-system)
2759 `(("pkg-config" ,pkg-config)
2760 ("r-knitr" ,r-knitr)))
2761 (home-page "https://r-forge.r-project.org/projects/rsymphony")
2762 (synopsis "Symphony integer linear programming solver in R")
2764 "This package was derived from Rsymphony. The package provides an R
2765 interface to SYMPHONY, a linear programming solver written in C++. The main
2766 difference between this package and Rsymphony is that it includes the solver
2767 source code, while Rsymphony expects to find header and library files on the
2768 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2769 to install interface to SYMPHONY.")
2770 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2771 ;; lpsimphony is released under the same terms.
2772 (license license:epl1.0)))
2774 (define-public r-ihw
2781 (uri (bioconductor-uri "IHW" version))
2784 "169ir0k1gygdh1wybwa0drdxnhrdrlyzzy0rkygi7jsirn69m74j"))))
2785 (properties `((upstream-name . "IHW")))
2786 (build-system r-build-system)
2788 `(("r-biocgenerics" ,r-biocgenerics)
2789 ("r-fdrtool" ,r-fdrtool)
2790 ("r-lpsymphony" ,r-lpsymphony)
2791 ("r-slam" ,r-slam)))
2793 `(("r-knitr" ,r-knitr)))
2794 (home-page "https://bioconductor.org/packages/IHW")
2795 (synopsis "Independent hypothesis weighting")
2797 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2798 procedure that increases power compared to the method of Benjamini and
2799 Hochberg by assigning data-driven weights to each hypothesis. The input to
2800 IHW is a two-column table of p-values and covariates. The covariate can be
2801 any continuous-valued or categorical variable that is thought to be
2802 informative on the statistical properties of each hypothesis test, while it is
2803 independent of the p-value under the null hypothesis.")
2804 (license license:artistic2.0)))
2806 (define-public r-icobra
2813 (uri (bioconductor-uri "iCOBRA" version))
2816 "0cvklagby3i221dlhyb51cciv0b3ch4a8z0wpm67q5n6n3k0cil1"))))
2817 (properties `((upstream-name . "iCOBRA")))
2818 (build-system r-build-system)
2820 `(("r-dplyr" ,r-dplyr)
2822 ("r-ggplot2" ,r-ggplot2)
2823 ("r-limma" ,r-limma)
2824 ("r-reshape2" ,r-reshape2)
2826 ("r-scales" ,r-scales)
2827 ("r-shiny" ,r-shiny)
2828 ("r-shinybs" ,r-shinybs)
2829 ("r-shinydashboard" ,r-shinydashboard)
2830 ("r-upsetr" ,r-upsetr)))
2832 `(("r-knitr" ,r-knitr)))
2833 (home-page "https://bioconductor.org/packages/iCOBRA")
2834 (synopsis "Comparison and visualization of ranking and assignment methods")
2836 "This package provides functions for calculation and visualization of
2837 performance metrics for evaluation of ranking and binary
2838 classification (assignment) methods. It also contains a Shiny application for
2839 interactive exploration of results.")
2840 (license license:gpl2+)))
2842 (define-public r-mast
2849 (uri (bioconductor-uri "MAST" version))
2852 "12d0q2fbq9d5jgyccmfv0cghv282s0j86wjfbnjpdf73fdrp6brr"))))
2853 (properties `((upstream-name . "MAST")))
2854 (build-system r-build-system)
2856 `(("r-abind" ,r-abind)
2857 ("r-biobase" ,r-biobase)
2858 ("r-biocgenerics" ,r-biocgenerics)
2859 ("r-data-table" ,r-data-table)
2860 ("r-ggplot2" ,r-ggplot2)
2862 ("r-progress" ,r-progress)
2863 ("r-reshape2" ,r-reshape2)
2864 ("r-s4vectors" ,r-s4vectors)
2865 ("r-singlecellexperiment" ,r-singlecellexperiment)
2866 ("r-stringr" ,r-stringr)
2867 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2869 `(("r-knitr" ,r-knitr)))
2870 (home-page "https://github.com/RGLab/MAST/")
2871 (synopsis "Model-based analysis of single cell transcriptomics")
2873 "This package provides methods and models for handling zero-inflated
2874 single cell assay data.")
2875 (license license:gpl2+)))
2877 (define-public r-monocle
2884 (uri (bioconductor-uri "monocle" version))
2887 "1vziidavlyhixmx6j7lf29qx8xcjwrc9q3x2f63gcff41q3jf9xd"))))
2888 (build-system r-build-system)
2890 `(("r-biobase" ,r-biobase)
2891 ("r-biocgenerics" ,r-biocgenerics)
2892 ("r-biocviews" ,r-biocviews)
2893 ("r-cluster" ,r-cluster)
2894 ("r-combinat" ,r-combinat)
2895 ("r-ddrtree" ,r-ddrtree)
2896 ("r-densityclust" ,r-densityclust)
2897 ("r-dplyr" ,r-dplyr)
2898 ("r-fastica" ,r-fastica)
2899 ("r-ggplot2" ,r-ggplot2)
2900 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2901 ("r-igraph" ,r-igraph)
2902 ("r-irlba" ,r-irlba)
2903 ("r-limma" ,r-limma)
2905 ("r-matrix" ,r-matrix)
2906 ("r-matrixstats" ,r-matrixstats)
2907 ("r-pheatmap" ,r-pheatmap)
2909 ("r-proxy" ,r-proxy)
2910 ("r-qlcmatrix" ,r-qlcmatrix)
2913 ("r-reshape2" ,r-reshape2)
2914 ("r-rtsne" ,r-rtsne)
2916 ("r-stringr" ,r-stringr)
2917 ("r-tibble" ,r-tibble)
2919 ("r-viridis" ,r-viridis)))
2921 `(("r-knitr" ,r-knitr)))
2922 (home-page "https://bioconductor.org/packages/monocle")
2923 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2925 "Monocle performs differential expression and time-series analysis for
2926 single-cell expression experiments. It orders individual cells according to
2927 progress through a biological process, without knowing ahead of time which
2928 genes define progress through that process. Monocle also performs
2929 differential expression analysis, clustering, visualization, and other useful
2930 tasks on single cell expression data. It is designed to work with RNA-Seq and
2931 qPCR data, but could be used with other types as well.")
2932 (license license:artistic2.0)))
2934 (define-public r-monocle3
2942 (url "https://github.com/cole-trapnell-lab/monocle3")
2944 (file-name (git-file-name name version))
2947 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2948 (build-system r-build-system)
2950 `(("r-biobase" ,r-biobase)
2951 ("r-biocgenerics" ,r-biocgenerics)
2952 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2953 ("r-dplyr" ,r-dplyr)
2954 ("r-ggplot2" ,r-ggplot2)
2955 ("r-ggrepel" ,r-ggrepel)
2957 ("r-htmlwidgets" ,r-htmlwidgets)
2958 ("r-igraph" ,r-igraph)
2959 ("r-irlba" ,r-irlba)
2960 ("r-limma" ,r-limma)
2961 ("r-lmtest" ,r-lmtest)
2963 ("r-matrix" ,r-matrix)
2964 ("r-matrix-utils" ,r-matrix-utils)
2965 ("r-pbapply" ,r-pbapply)
2966 ("r-pbmcapply" ,r-pbmcapply)
2967 ("r-pheatmap" ,r-pheatmap)
2968 ("r-plotly" ,r-plotly)
2970 ("r-proxy" ,r-proxy)
2972 ("r-purrr" ,r-purrr)
2975 ("r-rcppparallel" ,r-rcppparallel)
2976 ("r-reshape2" ,r-reshape2)
2977 ("r-reticulate" ,r-reticulate)
2978 ("r-rhpcblasctl" ,r-rhpcblasctl)
2979 ("r-rtsne" ,r-rtsne)
2980 ("r-shiny" ,r-shiny)
2982 ("r-spdep" ,r-spdep)
2983 ("r-speedglm" ,r-speedglm)
2984 ("r-stringr" ,r-stringr)
2985 ("r-singlecellexperiment" ,r-singlecellexperiment)
2986 ("r-tibble" ,r-tibble)
2987 ("r-tidyr" ,r-tidyr)
2989 ("r-viridis" ,r-viridis)))
2990 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2991 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2993 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2994 (license license:expat)))
2996 (define-public r-noiseq
3003 (uri (bioconductor-uri "NOISeq" version))
3006 "0lg3za0km6v9l6dxigbxx6nsx9y6m3dyzh9srngi53s8387vhj33"))))
3007 (properties `((upstream-name . "NOISeq")))
3008 (build-system r-build-system)
3010 `(("r-biobase" ,r-biobase)
3011 ("r-matrix" ,r-matrix)))
3012 (home-page "https://bioconductor.org/packages/NOISeq")
3013 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
3015 "This package provides tools to support the analysis of RNA-seq
3016 expression data or other similar kind of data. It provides exploratory plots
3017 to evaluate saturation, count distribution, expression per chromosome, type of
3018 detected features, features length, etc. It also supports the analysis of
3019 differential expression between two experimental conditions with no parametric
3021 (license license:artistic2.0)))
3023 (define-public r-scdd
3030 (uri (bioconductor-uri "scDD" version))
3033 "19q01jksxpv4p26wp2c6faa4fffkjnqlbcds2x955pk35jkqknxx"))))
3034 (properties `((upstream-name . "scDD")))
3035 (build-system r-build-system)
3038 ("r-biocparallel" ,r-biocparallel)
3039 ("r-ebseq" ,r-ebseq)
3040 ("r-fields" ,r-fields)
3041 ("r-ggplot2" ,r-ggplot2)
3042 ("r-mclust" ,r-mclust)
3043 ("r-outliers" ,r-outliers)
3044 ("r-s4vectors" ,r-s4vectors)
3045 ("r-scran" ,r-scran)
3046 ("r-singlecellexperiment" ,r-singlecellexperiment)
3047 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3049 `(("r-knitr" ,r-knitr)))
3050 (home-page "https://github.com/kdkorthauer/scDD")
3051 (synopsis "Mixture modeling of single-cell RNA-seq data")
3053 "This package implements a method to analyze single-cell RNA-seq data
3054 utilizing flexible Dirichlet Process mixture models. Genes with differential
3055 distributions of expression are classified into several interesting patterns
3056 of differences between two conditions. The package also includes functions
3057 for simulating data with these patterns from negative binomial
3059 (license license:gpl2)))
3061 (define-public r-scone
3068 (uri (bioconductor-uri "scone" version))
3071 "12hcmbpncm0l1yxhm3sgkqqfri7s5qc46ikv5qcj8pw5a42rkx3g"))))
3072 (build-system r-build-system)
3074 `(("r-aroma-light" ,r-aroma-light)
3075 ("r-biocparallel" ,r-biocparallel)
3077 ("r-class" ,r-class)
3078 ("r-cluster" ,r-cluster)
3079 ("r-compositions" ,r-compositions)
3080 ("r-diptest" ,r-diptest)
3081 ("r-edger" ,r-edger)
3083 ("r-gplots" ,r-gplots)
3084 ("r-hexbin" ,r-hexbin)
3085 ("r-limma" ,r-limma)
3086 ("r-matrixstats" ,r-matrixstats)
3087 ("r-mixtools" ,r-mixtools)
3088 ("r-rarpack" ,r-rarpack)
3089 ("r-rcolorbrewer" ,r-rcolorbrewer)
3090 ("r-rhdf5" ,r-rhdf5)
3091 ("r-ruvseq" ,r-ruvseq)
3092 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3094 `(("r-knitr" ,r-knitr)))
3095 (home-page "https://bioconductor.org/packages/scone")
3096 (synopsis "Single cell overview of normalized expression data")
3098 "SCONE is an R package for comparing and ranking the performance of
3099 different normalization schemes for single-cell RNA-seq and other
3100 high-throughput analyses.")
3101 (license license:artistic2.0)))
3103 (define-public r-geoquery
3110 (uri (bioconductor-uri "GEOquery" version))
3113 "0sap1dsa3k3qpv5z5y3cimxyhbm8qai87gqn3g1w3hwlcqsss92m"))))
3114 (properties `((upstream-name . "GEOquery")))
3115 (build-system r-build-system)
3117 `(("r-biobase" ,r-biobase)
3118 ("r-dplyr" ,r-dplyr)
3120 ("r-limma" ,r-limma)
3121 ("r-magrittr" ,r-magrittr)
3122 ("r-readr" ,r-readr)
3123 ("r-tidyr" ,r-tidyr)
3124 ("r-xml2" ,r-xml2)))
3126 `(("r-knitr" ,r-knitr)))
3127 (home-page "https://github.com/seandavi/GEOquery/")
3128 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
3130 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
3131 microarray data. Given the rich and varied nature of this resource, it is
3132 only natural to want to apply BioConductor tools to these data. GEOquery is
3133 the bridge between GEO and BioConductor.")
3134 (license license:gpl2)))
3136 (define-public r-illuminaio
3138 (name "r-illuminaio")
3143 (uri (bioconductor-uri "illuminaio" version))
3146 "0i587r1v5aa25w0jm1zvh7spc1gqmvza49i2kv00g1qzj8whq67c"))))
3147 (build-system r-build-system)
3149 `(("r-base64" ,r-base64)))
3150 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
3151 (synopsis "Parse Illumina microarray output files")
3153 "This package provides tools for parsing Illumina's microarray output
3154 files, including IDAT.")
3155 (license license:gpl2)))
3157 (define-public r-siggenes
3164 (uri (bioconductor-uri "siggenes" version))
3167 "0i4y1hgq1ljxkf6sypb6c8yp412a8q5v5z68cx1zrgxnccvp0mfy"))))
3168 (build-system r-build-system)
3170 `(("r-biobase" ,r-biobase)
3171 ("r-multtest" ,r-multtest)
3172 ("r-scrime" ,r-scrime)))
3173 (home-page "https://bioconductor.org/packages/siggenes/")
3175 "Multiple testing using SAM and Efron's empirical Bayes approaches")
3177 "This package provides tools for the identification of differentially
3178 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
3179 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
3180 Bayes Analyses of Microarrays} (EBAM).")
3181 (license license:lgpl2.0+)))
3183 (define-public r-bumphunter
3185 (name "r-bumphunter")
3190 (uri (bioconductor-uri "bumphunter" version))
3193 "04y6spdx89j3bsq2xniqd3sbfmakwc0klbpzjlp1q2xs9kywr4dq"))))
3194 (build-system r-build-system)
3196 `(("r-annotationdbi" ,r-annotationdbi)
3197 ("r-biocgenerics" ,r-biocgenerics)
3198 ("r-dorng" ,r-dorng)
3199 ("r-foreach" ,r-foreach)
3200 ("r-genomeinfodb" ,r-genomeinfodb)
3201 ("r-genomicfeatures" ,r-genomicfeatures)
3202 ("r-genomicranges" ,r-genomicranges)
3203 ("r-iranges" ,r-iranges)
3204 ("r-iterators" ,r-iterators)
3205 ("r-limma" ,r-limma)
3206 ("r-locfit" ,r-locfit)
3207 ("r-matrixstats" ,r-matrixstats)
3208 ("r-s4vectors" ,r-s4vectors)))
3209 (home-page "https://github.com/ririzarr/bumphunter")
3210 (synopsis "Find bumps in genomic data")
3212 "This package provides tools for finding bumps in genomic data in order
3213 to identify differentially methylated regions in epigenetic epidemiology
3215 (license license:artistic2.0)))
3217 (define-public r-minfi
3224 (uri (bioconductor-uri "minfi" version))
3227 "0bl1sk9syy770d5wqa0k1y0wrs5x8sbj13px1v03v3693pdj081w"))))
3228 (build-system r-build-system)
3230 `(("r-beanplot" ,r-beanplot)
3231 ("r-biobase" ,r-biobase)
3232 ("r-biocgenerics" ,r-biocgenerics)
3233 ("r-biocparallel" ,r-biocparallel)
3234 ("r-biostrings" ,r-biostrings)
3235 ("r-bumphunter" ,r-bumphunter)
3236 ("r-data-table" ,r-data-table)
3237 ("r-delayedarray" ,r-delayedarray)
3238 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3239 ("r-genefilter" ,r-genefilter)
3240 ("r-genomeinfodb" ,r-genomeinfodb)
3241 ("r-genomicranges" ,r-genomicranges)
3242 ("r-geoquery" ,r-geoquery)
3243 ("r-hdf5array" ,r-hdf5array)
3244 ("r-illuminaio" ,r-illuminaio)
3245 ("r-iranges" ,r-iranges)
3246 ("r-lattice" ,r-lattice)
3247 ("r-limma" ,r-limma)
3249 ("r-mclust" ,r-mclust)
3251 ("r-nor1mix" ,r-nor1mix)
3252 ("r-preprocesscore" ,r-preprocesscore)
3253 ("r-quadprog" ,r-quadprog)
3254 ("r-rcolorbrewer" ,r-rcolorbrewer)
3255 ("r-reshape" ,r-reshape)
3256 ("r-s4vectors" ,r-s4vectors)
3257 ("r-siggenes" ,r-siggenes)
3258 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3260 `(("r-knitr" ,r-knitr)))
3261 (home-page "https://github.com/hansenlab/minfi")
3262 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
3264 "This package provides tools to analyze and visualize Illumina Infinium
3265 methylation arrays.")
3266 (license license:artistic2.0)))
3268 (define-public r-methylumi
3270 (name "r-methylumi")
3275 (uri (bioconductor-uri "methylumi" version))
3278 "0phb2dyndnk9rv79nx246cn1sc9wbzdqqbgl6402knc7dgh799wr"))))
3279 (build-system r-build-system)
3281 `(("r-annotate" ,r-annotate)
3282 ("r-annotationdbi" ,r-annotationdbi)
3283 ("r-biobase" ,r-biobase)
3284 ("r-biocgenerics" ,r-biocgenerics)
3285 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
3286 ("r-genefilter" ,r-genefilter)
3287 ("r-genomeinfodb" ,r-genomeinfodb)
3288 ("r-genomicranges" ,r-genomicranges)
3289 ("r-ggplot2" ,r-ggplot2)
3290 ("r-illuminaio" ,r-illuminaio)
3291 ("r-iranges" ,r-iranges)
3292 ("r-lattice" ,r-lattice)
3293 ("r-matrixstats" ,r-matrixstats)
3294 ("r-minfi" ,r-minfi)
3295 ("r-reshape2" ,r-reshape2)
3296 ("r-s4vectors" ,r-s4vectors)
3297 ("r-scales" ,r-scales)
3298 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3300 `(("r-knitr" ,r-knitr)))
3301 (home-page "https://bioconductor.org/packages/methylumi")
3302 (synopsis "Handle Illumina methylation data")
3304 "This package provides classes for holding and manipulating Illumina
3305 methylation data. Based on eSet, it can contain MIAME information, sample
3306 information, feature information, and multiple matrices of data. An
3307 \"intelligent\" import function, methylumiR can read the Illumina text files
3308 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3309 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3310 background correction, and quality control features for GoldenGate, Infinium,
3311 and Infinium HD arrays are also included.")
3312 (license license:gpl2)))
3314 (define-public r-lumi
3321 (uri (bioconductor-uri "lumi" version))
3324 "196izc4mdh8j4f04fsf8cqm99w1inzpwy34kwvhz6zvxj2ywn1i9"))))
3325 (build-system r-build-system)
3327 `(("r-affy" ,r-affy)
3328 ("r-annotate" ,r-annotate)
3329 ("r-annotationdbi" ,r-annotationdbi)
3330 ("r-biobase" ,r-biobase)
3332 ("r-genomicfeatures" ,r-genomicfeatures)
3333 ("r-genomicranges" ,r-genomicranges)
3334 ("r-kernsmooth" ,r-kernsmooth)
3335 ("r-lattice" ,r-lattice)
3337 ("r-methylumi" ,r-methylumi)
3339 ("r-nleqslv" ,r-nleqslv)
3340 ("r-preprocesscore" ,r-preprocesscore)
3341 ("r-rsqlite" ,r-rsqlite)))
3342 (home-page "https://bioconductor.org/packages/lumi")
3343 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3345 "The lumi package provides an integrated solution for the Illumina
3346 microarray data analysis. It includes functions of Illumina
3347 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3348 variance stabilization, normalization and gene annotation at the probe level.
3349 It also includes the functions of processing Illumina methylation microarrays,
3350 especially Illumina Infinium methylation microarrays.")
3351 (license license:lgpl2.0+)))
3353 (define-public r-linnorm
3360 (uri (bioconductor-uri "Linnorm" version))
3363 "143hdfswp5sda5al1igrm5gyn7a6mp1j7hjm5jsc300335lm3kgp"))))
3364 (properties `((upstream-name . "Linnorm")))
3365 (build-system r-build-system)
3367 `(("r-amap" ,r-amap)
3368 ("r-apcluster" ,r-apcluster)
3369 ("r-ellipse" ,r-ellipse)
3370 ("r-fastcluster" ,r-fastcluster)
3372 ("r-ggdendro" ,r-ggdendro)
3373 ("r-ggplot2" ,r-ggplot2)
3374 ("r-gmodels" ,r-gmodels)
3375 ("r-igraph" ,r-igraph)
3376 ("r-limma" ,r-limma)
3378 ("r-mclust" ,r-mclust)
3380 ("r-rcpparmadillo" ,r-rcpparmadillo)
3381 ("r-rtsne" ,r-rtsne)
3382 ("r-statmod" ,r-statmod)
3383 ("r-vegan" ,r-vegan)
3386 `(("r-knitr" ,r-knitr)))
3387 (home-page "http://www.jjwanglab.org/Linnorm/")
3388 (synopsis "Linear model and normality based transformation method")
3390 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3391 count data or any large scale count data. It transforms such datasets for
3392 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3393 the following pipelines are implemented:
3396 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3397 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3398 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3399 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3400 @item Differential expression analysis or differential peak detection using
3401 limma (@code{Linnorm.limma})
3402 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3403 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3404 @item Stable gene selection for scRNA-seq data; for users without or who do
3405 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3406 @item Data imputation (@code{Linnorm.DataImput}).
3409 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3410 @code{RnaXSim} function is included for simulating RNA-seq data for the
3411 evaluation of DEG analysis methods.")
3412 (license license:expat)))
3414 (define-public r-ioniser
3421 (uri (bioconductor-uri "IONiseR" version))
3424 "05fndlblczabva60gn6h0dijqxyn0wknrv8a925fgc4bn415g31w"))))
3425 (properties `((upstream-name . "IONiseR")))
3426 (build-system r-build-system)
3428 `(("r-biocgenerics" ,r-biocgenerics)
3429 ("r-biocparallel" ,r-biocparallel)
3430 ("r-biostrings" ,r-biostrings)
3431 ("r-bit64" ,r-bit64)
3432 ("r-dplyr" ,r-dplyr)
3433 ("r-ggplot2" ,r-ggplot2)
3434 ("r-magrittr" ,r-magrittr)
3435 ("r-rhdf5" ,r-rhdf5)
3436 ("r-shortread" ,r-shortread)
3437 ("r-stringr" ,r-stringr)
3438 ("r-tibble" ,r-tibble)
3439 ("r-tidyr" ,r-tidyr)
3440 ("r-xvector" ,r-xvector)))
3442 `(("r-knitr" ,r-knitr)))
3443 (home-page "https://bioconductor.org/packages/IONiseR/")
3444 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3446 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3447 MinION data. It extracts summary statistics from a set of fast5 files and can
3448 be used either before or after base calling. In addition to standard
3449 summaries of the read-types produced, it provides a number of plots for
3450 visualising metrics relative to experiment run time or spatially over the
3451 surface of a flowcell.")
3452 (license license:expat)))
3454 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3455 (define-public r-gkmsvm
3462 (uri (cran-uri "gkmSVM" version))
3465 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
3466 (properties `((upstream-name . "gkmSVM")))
3467 (build-system r-build-system)
3469 `(("r-kernlab" ,r-kernlab)
3472 ("r-seqinr" ,r-seqinr)))
3473 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3474 (synopsis "Gapped-kmer support vector machine")
3476 "This R package provides tools for training gapped-kmer SVM classifiers
3477 for DNA and protein sequences. This package supports several sequence
3478 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3479 (license license:gpl2+)))
3481 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
3482 (define-public r-mutoss
3489 (uri (cran-uri "mutoss" version))
3492 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3493 (properties `((upstream-name . "mutoss")))
3494 (build-system r-build-system)
3496 `(("r-multcomp" ,r-multcomp)
3497 ("r-multtest" ,r-multtest)
3498 ("r-mvtnorm" ,r-mvtnorm)
3499 ("r-plotrix" ,r-plotrix)))
3500 (home-page "https://github.com/kornl/mutoss/")
3501 (synopsis "Unified multiple testing procedures")
3503 "This package is designed to ease the application and comparison of
3504 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3505 are standardized and usable by the accompanying mutossGUI package.")
3506 ;; Any version of the GPL.
3507 (license (list license:gpl2+ license:gpl3+))))
3509 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3510 ;; from Bioconductor, so we put it here.
3511 (define-public r-metap
3518 (uri (cran-uri "metap" version))
3521 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
3522 (build-system r-build-system)
3524 `(("r-lattice" ,r-lattice)
3525 ("r-mutoss" ,r-mutoss)
3526 ("r-rdpack" ,r-rdpack)
3527 ("r-tfisher" ,r-tfisher)))
3528 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3529 (synopsis "Meta-analysis of significance values")
3531 "The canonical way to perform meta-analysis involves using effect sizes.
3532 When they are not available this package provides a number of methods for
3533 meta-analysis of significance values including the methods of Edgington,
3534 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3535 published results; and a routine for graphical display.")
3536 (license license:gpl2)))
3538 (define-public r-triform
3545 (uri (bioconductor-uri "triform" version))
3548 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
3549 (build-system r-build-system)
3551 `(("r-biocgenerics" ,r-biocgenerics)
3552 ("r-iranges" ,r-iranges)
3553 ("r-yaml" ,r-yaml)))
3554 (home-page "https://bioconductor.org/packages/triform/")
3555 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3557 "The Triform algorithm uses model-free statistics to identify peak-like
3558 distributions of TF ChIP sequencing reads, taking advantage of an improved
3559 peak definition in combination with known profile characteristics.")
3560 (license license:gpl2)))
3562 (define-public r-varianttools
3564 (name "r-varianttools")
3569 (uri (bioconductor-uri "VariantTools" version))
3572 "0g93rljlmhk1d53z0bgi84i2cn5c3r1dpm8id2pv0nk9ncdh3yxx"))))
3573 (properties `((upstream-name . "VariantTools")))
3574 (build-system r-build-system)
3576 `(("r-biobase" ,r-biobase)
3577 ("r-biocgenerics" ,r-biocgenerics)
3578 ("r-biocparallel" ,r-biocparallel)
3579 ("r-biostrings" ,r-biostrings)
3580 ("r-bsgenome" ,r-bsgenome)
3581 ("r-genomeinfodb" ,r-genomeinfodb)
3582 ("r-genomicfeatures" ,r-genomicfeatures)
3583 ("r-genomicranges" ,r-genomicranges)
3584 ("r-iranges" ,r-iranges)
3585 ("r-matrix" ,r-matrix)
3586 ("r-rsamtools" ,r-rsamtools)
3587 ("r-rtracklayer" ,r-rtracklayer)
3588 ("r-s4vectors" ,r-s4vectors)
3589 ("r-variantannotation" ,r-variantannotation)))
3590 (home-page "https://bioconductor.org/packages/VariantTools/")
3591 (synopsis "Tools for exploratory analysis of variant calls")
3593 "Explore, diagnose, and compare variant calls using filters. The
3594 VariantTools package supports a workflow for loading data, calling single
3595 sample variants and tumor-specific somatic mutations or other sample-specific
3596 variant types (e.g., RNA editing). Most of the functions operate on
3597 alignments (BAM files) or datasets of called variants. The user is expected
3598 to have already aligned the reads with a separate tool, e.g., GSNAP via
3600 (license license:artistic2.0)))
3602 (define-public r-heatplus
3609 (uri (bioconductor-uri "Heatplus" version))
3612 "12nd0h8svx7qydv1shk0gdpvnbixf7qi6zh06881wsmxf5s970rw"))))
3613 (properties `((upstream-name . "Heatplus")))
3614 (build-system r-build-system)
3616 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3617 (home-page "https://github.com/alexploner/Heatplus")
3618 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3620 "This package provides tools to display a rectangular heatmap (intensity
3621 plot) of a data matrix. By default, both samples (columns) and features (row)
3622 of the matrix are sorted according to a hierarchical clustering, and the
3623 corresponding dendrogram is plotted. Optionally, panels with additional
3624 information about samples and features can be added to the plot.")
3625 (license license:gpl2+)))
3627 (define-public r-gosemsim
3634 (uri (bioconductor-uri "GOSemSim" version))
3637 "0v4q9xr1cm5xr08pgbzrss41kh3yz7xyh31n55l0sjmr1629ykln"))))
3638 (properties `((upstream-name . "GOSemSim")))
3639 (build-system r-build-system)
3641 `(("r-annotationdbi" ,r-annotationdbi)
3642 ("r-go-db" ,r-go-db)
3643 ("r-rcpp" ,r-rcpp)))
3645 `(("r-knitr" ,r-knitr)))
3646 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3647 (synopsis "GO-terms semantic similarity measures")
3649 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3650 quantitative ways to compute similarities between genes and gene groups, and
3651 have became important basis for many bioinformatics analysis approaches.
3652 GOSemSim is an R package for semantic similarity computation among GO terms,
3653 sets of GO terms, gene products and gene clusters.")
3654 (license license:artistic2.0)))
3656 (define-public r-anota
3663 (uri (bioconductor-uri "anota" version))
3666 "1ind5cyq85l63xpqmg2n9rg805s5amh48iiw05zqr8kih6hlilpm"))))
3667 (build-system r-build-system)
3669 `(("r-multtest" ,r-multtest)
3670 ("r-qvalue" ,r-qvalue)))
3671 (home-page "https://bioconductor.org/packages/anota/")
3672 (synopsis "Analysis of translational activity")
3674 "Genome wide studies of translational control is emerging as a tool to
3675 study various biological conditions. The output from such analysis is both
3676 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3677 involved in translation (the actively translating mRNA level) for each mRNA.
3678 The standard analysis of such data strives towards identifying differential
3679 translational between two or more sample classes - i.e. differences in
3680 actively translated mRNA levels that are independent of underlying differences
3681 in cytosolic mRNA levels. This package allows for such analysis using partial
3682 variances and the random variance model. As 10s of thousands of mRNAs are
3683 analyzed in parallel the library performs a number of tests to assure that
3684 the data set is suitable for such analysis.")
3685 (license license:gpl3)))
3687 (define-public r-sigpathway
3689 (name "r-sigpathway")
3694 (uri (bioconductor-uri "sigPathway" version))
3697 "0a79sdvag80p7xcdz8mp8wiby36yxmappzycfd2rp36v9drjk0h5"))))
3698 (properties `((upstream-name . "sigPathway")))
3699 (build-system r-build-system)
3700 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3701 (synopsis "Pathway analysis")
3703 "This package is used to conduct pathway analysis by calculating the NT_k
3704 and NE_k statistics in a statistical framework for determining whether a
3705 specified group of genes for a pathway has a coordinated association with a
3706 phenotype of interest.")
3707 (license license:gpl2)))
3709 (define-public r-fgsea
3716 (uri (bioconductor-uri "fgsea" version))
3719 "0zbjj8al1ps7immxixsn5g8lvbmpmxvqwqbpdgsicxp00gb9bybc"))))
3720 (build-system r-build-system)
3723 ("r-biocparallel" ,r-biocparallel)
3724 ("r-data-table" ,r-data-table)
3725 ("r-fastmatch" ,r-fastmatch)
3726 ("r-ggplot2" ,r-ggplot2)
3727 ("r-gridextra" ,r-gridextra)
3728 ("r-matrix" ,r-matrix)
3729 ("r-rcpp" ,r-rcpp)))
3731 `(("r-knitr" ,r-knitr)))
3732 (home-page "https://github.com/ctlab/fgsea/")
3733 (synopsis "Fast gene set enrichment analysis")
3735 "The package implements an algorithm for fast gene set enrichment
3736 analysis. Using the fast algorithm makes more permutations and gets
3737 more fine grained p-values, which allows using accurate standard approaches
3738 to multiple hypothesis correction.")
3739 (license license:expat)))
3741 (define-public r-dose
3748 (uri (bioconductor-uri "DOSE" version))
3751 "1j0wcg7w2ns3ag9d272cqlg3j62ag2xnc5gfsjl6g2ij5xkvylb8"))))
3752 (properties `((upstream-name . "DOSE")))
3753 (build-system r-build-system)
3755 `(("r-annotationdbi" ,r-annotationdbi)
3756 ("r-biocparallel" ,r-biocparallel)
3757 ("r-do-db" ,r-do-db)
3758 ("r-fgsea" ,r-fgsea)
3759 ("r-ggplot2" ,r-ggplot2)
3760 ("r-gosemsim" ,r-gosemsim)
3761 ("r-qvalue" ,r-qvalue)
3762 ("r-reshape2" ,r-reshape2)))
3764 `(("r-knitr" ,r-knitr)))
3765 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3766 (synopsis "Disease ontology semantic and enrichment analysis")
3768 "This package implements five methods proposed by Resnik, Schlicker,
3769 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3770 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3771 including hypergeometric model and gene set enrichment analysis are also
3772 implemented for discovering disease associations of high-throughput biological
3774 (license license:artistic2.0)))
3776 (define-public r-enrichplot
3778 (name "r-enrichplot")
3783 (uri (bioconductor-uri "enrichplot" version))
3786 "01m3cp717ldfbz5w3yfywvjg6sfjzz7s3vlk7w268lmmcg6g6bz7"))))
3787 (build-system r-build-system)
3789 `(("r-annotationdbi" ,r-annotationdbi)
3790 ("r-cowplot" ,r-cowplot)
3792 ("r-europepmc" ,r-europepmc)
3793 ("r-ggplot2" ,r-ggplot2)
3794 ("r-ggplotify" ,r-ggplotify)
3795 ("r-ggraph" ,r-ggraph)
3796 ("r-ggridges" ,r-ggridges)
3797 ("r-gosemsim" ,r-gosemsim)
3798 ("r-gridextra" ,r-gridextra)
3799 ("r-igraph" ,r-igraph)
3801 ("r-purrr" ,r-purrr)
3802 ("r-rcolorbrewer" ,r-rcolorbrewer)
3803 ("r-reshape2" ,r-reshape2)
3804 ("r-scatterpie" ,r-scatterpie)))
3806 `(("r-knitr" ,r-knitr)))
3807 (home-page "https://github.com/GuangchuangYu/enrichplot")
3808 (synopsis "Visualization of functional enrichment result")
3810 "The enrichplot package implements several visualization methods for
3811 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3812 All the visualization methods are developed based on ggplot2 graphics.")
3813 (license license:artistic2.0)))
3815 (define-public r-clusterprofiler
3817 (name "r-clusterprofiler")
3822 (uri (bioconductor-uri "clusterProfiler" version))
3825 "11zsgb8wbdv8r4c04iczz4aala4yw4ai7rz8igdzz87c0940nxkb"))))
3827 `((upstream-name . "clusterProfiler")))
3828 (build-system r-build-system)
3830 `(("r-annotationdbi" ,r-annotationdbi)
3832 ("r-downloader" ,r-downloader)
3833 ("r-dplyr" ,r-dplyr)
3834 ("r-enrichplot" ,r-enrichplot)
3835 ("r-go-db" ,r-go-db)
3836 ("r-gosemsim" ,r-gosemsim)
3837 ("r-magrittr" ,r-magrittr)
3839 ("r-qvalue" ,r-qvalue)
3840 ("r-rlang" ,r-rlang)
3841 ("r-rvcheck" ,r-rvcheck)
3842 ("r-tidyr" ,r-tidyr)))
3844 `(("r-knitr" ,r-knitr)))
3845 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3846 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3848 "This package implements methods to analyze and visualize functional
3849 profiles (GO and KEGG) of gene and gene clusters.")
3850 (license license:artistic2.0)))
3852 (define-public r-mlinterfaces
3854 (name "r-mlinterfaces")
3859 (uri (bioconductor-uri "MLInterfaces" version))
3862 "0x3mnvb5a6kri4q5w0wfmx02v79my08zhmkaik9pqlprd7y5wynq"))))
3863 (properties `((upstream-name . "MLInterfaces")))
3864 (build-system r-build-system)
3866 `(("r-annotate" ,r-annotate)
3867 ("r-biobase" ,r-biobase)
3868 ("r-biocgenerics" ,r-biocgenerics)
3869 ("r-cluster" ,r-cluster)
3872 ("r-gdata" ,r-gdata)
3873 ("r-genefilter" ,r-genefilter)
3874 ("r-ggvis" ,r-ggvis)
3875 ("r-hwriter" ,r-hwriter)
3877 ("r-mlbench" ,r-mlbench)
3879 ("r-rcolorbrewer" ,r-rcolorbrewer)
3881 ("r-rpart" ,r-rpart)
3882 ("r-sfsmisc" ,r-sfsmisc)
3883 ("r-shiny" ,r-shiny)
3884 ("r-threejs" ,r-threejs)))
3885 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3886 (synopsis "Interfaces to R machine learning procedures")
3888 "This package provides uniform interfaces to machine learning code for
3889 data in R and Bioconductor containers.")
3890 ;; Any version of the LGPL.
3891 (license license:lgpl2.1+)))
3893 (define-public r-annaffy
3900 (uri (bioconductor-uri "annaffy" version))
3903 "1rc9fb83by9jfgwfj2zhhbj93v296blwd8jl2rh7jj200mrpznn4"))))
3904 (build-system r-build-system)
3907 (modify-phases %standard-phases
3908 (add-after 'unpack 'remove-reference-to-non-free-data
3910 (substitute* "DESCRIPTION"
3914 `(("r-annotationdbi" ,r-annotationdbi)
3915 ("r-biobase" ,r-biobase)
3917 ("r-go-db" ,r-go-db)))
3918 (home-page "https://bioconductor.org/packages/annaffy/")
3919 (synopsis "Annotation tools for Affymetrix biological metadata")
3921 "This package provides functions for handling data from Bioconductor
3922 Affymetrix annotation data packages. It produces compact HTML and text
3923 reports including experimental data and URL links to many online databases.
3924 It allows searching of biological metadata using various criteria.")
3925 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3926 ;; the LGPL 2.1 is included.
3927 (license license:lgpl2.1+)))
3929 (define-public r-a4core
3936 (uri (bioconductor-uri "a4Core" version))
3939 "1hn9lkaib1bx5n52as882f8zwsln8w40sx8hxbrnimjvgfxrbvnp"))))
3940 (properties `((upstream-name . "a4Core")))
3941 (build-system r-build-system)
3943 `(("r-biobase" ,r-biobase)
3944 ("r-glmnet" ,r-glmnet)))
3945 (home-page "https://bioconductor.org/packages/a4Core")
3946 (synopsis "Automated Affymetrix array analysis core package")
3948 "This is the core package for the automated analysis of Affymetrix
3950 (license license:gpl3)))
3952 (define-public r-a4classif
3954 (name "r-a4classif")
3959 (uri (bioconductor-uri "a4Classif" version))
3962 "0bj8m4nprw3maahd1qx9jjdxfip9ihbbpydbzwjxn6dlgw2i8mcr"))))
3963 (properties `((upstream-name . "a4Classif")))
3964 (build-system r-build-system)
3966 `(("r-a4core" ,r-a4core)
3967 ("r-a4preproc" ,r-a4preproc)
3968 ("r-glmnet" ,r-glmnet)
3969 ("r-mlinterfaces" ,r-mlinterfaces)
3972 ("r-varselrf" ,r-varselrf)))
3973 (home-page "https://bioconductor.org/packages/a4Classif/")
3974 (synopsis "Automated Affymetrix array analysis classification package")
3976 "This is the classification package for the automated analysis of
3977 Affymetrix arrays.")
3978 (license license:gpl3)))
3980 (define-public r-a4preproc
3982 (name "r-a4preproc")
3987 (uri (bioconductor-uri "a4Preproc" version))
3990 "1hy3jvhdjyjzzmw5wkil3cs26hvqnb056r09x0p2bjg5sc9hh8b8"))))
3991 (properties `((upstream-name . "a4Preproc")))
3992 (build-system r-build-system)
3994 `(("r-annotationdbi" ,r-annotationdbi)))
3995 (home-page "https://bioconductor.org/packages/a4Preproc/")
3996 (synopsis "Automated Affymetrix array analysis preprocessing package")
3998 "This is a package for the automated analysis of Affymetrix arrays. It
3999 is used for preprocessing the arrays.")
4000 (license license:gpl3)))
4002 (define-public r-a4reporting
4004 (name "r-a4reporting")
4009 (uri (bioconductor-uri "a4Reporting" version))
4012 "1jhlxqwfbgflcyzy9gyxznzcadj9zxchl3lfdlc4ffm0hwz5jl2f"))))
4013 (properties `((upstream-name . "a4Reporting")))
4014 (build-system r-build-system)
4016 `(("r-annaffy" ,r-annaffy)
4017 ("r-xtable" ,r-xtable)))
4018 (home-page "https://bioconductor.org/packages/a4Reporting/")
4019 (synopsis "Automated Affymetrix array analysis reporting package")
4021 "This is a package for the automated analysis of Affymetrix arrays. It
4022 provides reporting features.")
4023 (license license:gpl3)))
4025 (define-public r-a4base
4032 (uri (bioconductor-uri "a4Base" version))
4035 "0b7fy1wcydb9z43wb1663skswvhivn7ji15g00gqcshwkkiq4x02"))))
4036 (properties `((upstream-name . "a4Base")))
4037 (build-system r-build-system)
4039 `(("r-a4core" ,r-a4core)
4040 ("r-a4preproc" ,r-a4preproc)
4041 ("r-annaffy" ,r-annaffy)
4042 ("r-annotationdbi" ,r-annotationdbi)
4043 ("r-biobase" ,r-biobase)
4044 ("r-genefilter" ,r-genefilter)
4045 ("r-glmnet" ,r-glmnet)
4046 ("r-gplots" ,r-gplots)
4047 ("r-limma" ,r-limma)
4049 ("r-multtest" ,r-multtest)))
4050 (home-page "https://bioconductor.org/packages/a4Base/")
4051 (synopsis "Automated Affymetrix array analysis base package")
4053 "This package provides basic features for the automated analysis of
4054 Affymetrix arrays.")
4055 (license license:gpl3)))
4064 (uri (bioconductor-uri "a4" version))
4067 "1rzxg1h48jnlwqfjyyqzz6i3zlkfzc0i714rfplry7dyni6asgr7"))))
4068 (build-system r-build-system)
4070 `(("r-a4base" ,r-a4base)
4071 ("r-a4classif" ,r-a4classif)
4072 ("r-a4core" ,r-a4core)
4073 ("r-a4preproc" ,r-a4preproc)
4074 ("r-a4reporting" ,r-a4reporting)))
4075 (home-page "https://bioconductor.org/packages/a4/")
4076 (synopsis "Automated Affymetrix array analysis umbrella package")
4078 "This package provides a software suite for the automated analysis of
4079 Affymetrix arrays.")
4080 (license license:gpl3)))
4082 (define-public r-abseqr
4089 (uri (bioconductor-uri "abseqR" version))
4092 "0pzyfn0jv41rja6l4jbgwgsqy0q1d3kz23m9m6pc67p2a231i9c5"))))
4093 (properties `((upstream-name . "abseqR")))
4094 (build-system r-build-system)
4096 `(("pandoc" ,pandoc)
4097 ("pandoc-citeproc" ,pandoc-citeproc)))
4099 `(("r-biocparallel" ,r-biocparallel)
4100 ("r-biocstyle" ,r-biocstyle)
4101 ("r-circlize" ,r-circlize)
4102 ("r-flexdashboard" ,r-flexdashboard)
4103 ("r-ggcorrplot" ,r-ggcorrplot)
4104 ("r-ggdendro" ,r-ggdendro)
4105 ("r-ggplot2" ,r-ggplot2)
4106 ("r-gridextra" ,r-gridextra)
4107 ("r-knitr" ,r-knitr)
4108 ("r-plotly" ,r-plotly)
4111 ("r-rcolorbrewer" ,r-rcolorbrewer)
4112 ("r-reshape2" ,r-reshape2)
4113 ("r-rmarkdown" ,r-rmarkdown)
4114 ("r-stringr" ,r-stringr)
4115 ("r-vegan" ,r-vegan)
4116 ("r-venndiagram" ,r-venndiagram)))
4118 `(("r-knitr" ,r-knitr)))
4119 (home-page "https://github.com/malhamdoosh/abseqR")
4120 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
4122 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
4123 sequencing datasets generated from antibody libraries and abseqR is one of its
4124 packages. AbseqR empowers the users of abseqPy with plotting and reporting
4125 capabilities and allows them to generate interactive HTML reports for the
4126 convenience of viewing and sharing with other researchers. Additionally,
4127 abseqR extends abseqPy to compare multiple repertoire analyses and perform
4128 further downstream analysis on its output.")
4129 (license license:gpl3)))
4131 (define-public r-bacon
4138 (uri (bioconductor-uri "bacon" version))
4141 "066b9vyp8ivnzm9741mb5z763a7z40ar9m8w31yw84fjiv01v3dl"))))
4142 (build-system r-build-system)
4144 `(("r-biocparallel" ,r-biocparallel)
4145 ("r-ellipse" ,r-ellipse)
4146 ("r-ggplot2" ,r-ggplot2)))
4148 `(("r-knitr" ,r-knitr)))
4149 (home-page "https://bioconductor.org/packages/bacon/")
4150 (synopsis "Controlling bias and inflation in association studies")
4152 "Bacon can be used to remove inflation and bias often observed in
4153 epigenome- and transcriptome-wide association studies. To this end bacon
4154 constructs an empirical null distribution using a Gibbs Sampling algorithm by
4155 fitting a three-component normal mixture on z-scores.")
4156 (license license:gpl2+)))
4158 (define-public r-rgadem
4165 (uri (bioconductor-uri "rGADEM" version))
4168 "14mflbwhhj9f3b05zdlsdjwxmpb120r23fy306qkvxjprdqn4sz8"))))
4169 (properties `((upstream-name . "rGADEM")))
4170 (build-system r-build-system)
4172 `(("r-biostrings" ,r-biostrings)
4173 ("r-bsgenome" ,r-bsgenome)
4174 ("r-genomicranges" ,r-genomicranges)
4175 ("r-iranges" ,r-iranges)
4176 ("r-seqlogo" ,r-seqlogo)))
4177 (home-page "https://bioconductor.org/packages/rGADEM/")
4178 (synopsis "De novo sequence motif discovery")
4180 "rGADEM is an efficient de novo motif discovery tool for large-scale
4181 genomic sequence data.")
4182 (license license:artistic2.0)))
4184 (define-public r-motiv
4191 (uri (bioconductor-uri "MotIV" version))
4194 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
4195 (properties `((upstream-name . "MotIV")))
4196 (build-system r-build-system)
4200 `(("r-biocgenerics" ,r-biocgenerics)
4201 ("r-biostrings" ,r-biostrings)
4202 ("r-genomicranges" ,r-genomicranges)
4203 ("r-iranges" ,r-iranges)
4204 ("r-lattice" ,r-lattice)
4205 ("r-rgadem" ,r-rgadem)
4206 ("r-s4vectors" ,r-s4vectors)))
4207 (home-page "https://bioconductor.org/packages/MotIV/")
4208 (synopsis "Motif identification and validation")
4210 "This package is used for the identification and validation of sequence
4211 motifs. It makes use of STAMP for comparing a set of motifs to a given
4212 database (e.g. JASPAR). It can also be used to visualize motifs, motif
4213 distributions, modules and filter motifs.")
4214 (license license:gpl2)))
4216 (define-public r-motifdb
4222 (uri (bioconductor-uri "MotifDb" version))
4224 (base32 "0ixmdqp0s0xv9ar85n2wirbbssrzlk8a892wam55jdsf9y8aabkm"))))
4225 (properties `((upstream-name . "MotifDb")))
4226 (build-system r-build-system)
4228 `(("r-biocgenerics" ,r-biocgenerics)
4229 ("r-biostrings" ,r-biostrings)
4230 ("r-genomicranges" ,r-genomicranges)
4231 ("r-iranges" ,r-iranges)
4232 ("r-rtracklayer" ,r-rtracklayer)
4233 ("r-s4vectors" ,r-s4vectors)
4234 ("r-splitstackshape" ,r-splitstackshape)))
4236 `(("r-knitr" ,r-knitr)))
4237 (home-page "https://www.bioconductor.org/packages/MotifDb/")
4238 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
4239 (description "This package provides more than 2000 annotated position
4240 frequency matrices from nine public sources, for multiple organisms.")
4241 (license license:artistic2.0)))
4243 (define-public r-motifbreakr
4245 (name "r-motifbreakr")
4249 (uri (bioconductor-uri "motifbreakR" version))
4251 (base32 "09czgmyjcycsvyvadpjddwwvqvxzd0ba3zhczh4mqc09gwa6vhlm"))))
4252 (properties `((upstream-name . "motifbreakR")))
4253 (build-system r-build-system)
4255 `(("r-biocgenerics" ,r-biocgenerics)
4256 ("r-biocparallel" ,r-biocparallel)
4257 ("r-biostrings" ,r-biostrings)
4258 ("r-bsgenome" ,r-bsgenome)
4259 ("r-genomeinfodb" ,r-genomeinfodb)
4260 ("r-genomicranges" ,r-genomicranges)
4261 ("r-grimport" ,r-grimport)
4263 ("r-iranges" ,r-iranges)
4264 ("r-matrixstats" ,r-matrixstats)
4265 ("r-motifdb" ,r-motifdb)
4266 ("r-motifstack" ,r-motifstack)
4267 ("r-rtracklayer" ,r-rtracklayer)
4268 ("r-s4vectors" ,r-s4vectors)
4269 ("r-stringr" ,r-stringr)
4270 ("r-summarizedexperiment" ,r-summarizedexperiment)
4271 ("r-tfmpvalue" ,r-tfmpvalue)
4272 ("r-variantannotation" ,r-variantannotation)))
4274 `(("r-knitr" ,r-knitr)))
4275 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
4276 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
4277 (description "This package allows biologists to judge in the first place
4278 whether the sequence surrounding the polymorphism is a good match, and in
4279 the second place how much information is gained or lost in one allele of
4280 the polymorphism relative to another. This package gives a choice of
4281 algorithms for interrogation of genomes with motifs from public sources:
4283 @item a weighted-sum probability matrix;
4284 @item log-probabilities;
4285 @item weighted by relative entropy.
4288 This package can predict effects for novel or previously described variants in
4289 public databases, making it suitable for tasks beyond the scope of its original
4290 design. Lastly, it can be used to interrogate any genome curated within
4292 (license license:gpl2+)))
4294 (define-public r-motifstack
4296 (name "r-motifstack")
4301 (uri (bioconductor-uri "motifStack" version))
4304 "02vmkgn36n5xpmizy33znlzgmi3w5hnhsibgisbnhwwgxpkrwpcd"))))
4305 (properties `((upstream-name . "motifStack")))
4306 (build-system r-build-system)
4308 `(("r-ade4" ,r-ade4)
4309 ("r-biostrings" ,r-biostrings)
4310 ("r-ggplot2" ,r-ggplot2)
4311 ("r-grimport2" ,r-grimport2)
4312 ("r-htmlwidgets" ,r-htmlwidgets)
4313 ("r-motiv" ,r-motiv)
4314 ("r-scales" ,r-scales)
4317 `(("r-knitr" ,r-knitr)))
4318 (home-page "https://bioconductor.org/packages/motifStack/")
4319 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
4321 "The motifStack package is designed for graphic representation of
4322 multiple motifs with different similarity scores. It works with both DNA/RNA
4323 sequence motifs and amino acid sequence motifs. In addition, it provides the
4324 flexibility for users to customize the graphic parameters such as the font
4325 type and symbol colors.")
4326 (license license:gpl2+)))
4328 (define-public r-genomicscores
4330 (name "r-genomicscores")
4335 (uri (bioconductor-uri "GenomicScores" version))
4338 "0si2lgc37mkah4w990q1q2bf8xmshxj7cbx92bcrp0zaipjr96bb"))))
4339 (properties `((upstream-name . "GenomicScores")))
4340 (build-system r-build-system)
4342 `(("r-annotationhub" ,r-annotationhub)
4343 ("r-biobase" ,r-biobase)
4344 ("r-biocgenerics" ,r-biocgenerics)
4345 ("r-biostrings" ,r-biostrings)
4346 ("r-delayedarray" ,r-delayedarray)
4347 ("r-genomeinfodb" ,r-genomeinfodb)
4348 ("r-genomicranges" ,r-genomicranges)
4349 ("r-hdf5array" ,r-hdf5array)
4350 ("r-iranges" ,r-iranges)
4351 ("r-rhdf5" ,r-rhdf5)
4352 ("r-s4vectors" ,r-s4vectors)
4355 `(("r-knitr" ,r-knitr)))
4356 (home-page "https://github.com/rcastelo/GenomicScores/")
4357 (synopsis "Work with genome-wide position-specific scores")
4359 "This package provides infrastructure to store and access genome-wide
4360 position-specific scores within R and Bioconductor.")
4361 (license license:artistic2.0)))
4363 (define-public r-atacseqqc
4365 (name "r-atacseqqc")
4370 (uri (bioconductor-uri "ATACseqQC" version))
4373 "1gs9862hhh4gr1akij6ykhcj29s9dzg1vnj87hqrm19dfgl43qbh"))))
4374 (properties `((upstream-name . "ATACseqQC")))
4375 (build-system r-build-system)
4377 `(("r-biocgenerics" ,r-biocgenerics)
4378 ("r-biostrings" ,r-biostrings)
4379 ("r-bsgenome" ,r-bsgenome)
4380 ("r-chippeakanno" ,r-chippeakanno)
4381 ("r-edger" ,r-edger)
4382 ("r-genomeinfodb" ,r-genomeinfodb)
4383 ("r-genomicalignments" ,r-genomicalignments)
4384 ("r-genomicranges" ,r-genomicranges)
4385 ("r-genomicscores" ,r-genomicscores)
4386 ("r-iranges" ,r-iranges)
4387 ("r-kernsmooth" ,r-kernsmooth)
4388 ("r-limma" ,r-limma)
4389 ("r-motifstack" ,r-motifstack)
4390 ("r-preseqr" ,r-preseqr)
4391 ("r-randomforest" ,r-randomforest)
4392 ("r-rsamtools" ,r-rsamtools)
4393 ("r-rtracklayer" ,r-rtracklayer)
4394 ("r-s4vectors" ,r-s4vectors)))
4396 `(("r-knitr" ,r-knitr)))
4397 (home-page "https://bioconductor.org/packages/ATACseqQC/")
4398 (synopsis "ATAC-seq quality control")
4400 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
4401 sequencing, is a rapid and sensitive method for chromatin accessibility
4402 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
4403 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
4404 assess whether their ATAC-seq experiment is successful. It includes
4405 diagnostic plots of fragment size distribution, proportion of mitochondria
4406 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
4408 (license license:gpl2+)))
4410 (define-public r-gofuncr
4417 (uri (bioconductor-uri "GOfuncR" version))
4420 "1ixjkqb9wpwqfzxsg0h96c6fa63wrk72sfh6x4pq0kpyrcc0ind1"))))
4421 (properties `((upstream-name . "GOfuncR")))
4422 (build-system r-build-system)
4424 `(("r-annotationdbi" ,r-annotationdbi)
4425 ("r-genomicranges" ,r-genomicranges)
4426 ("r-gtools" ,r-gtools)
4427 ("r-iranges" ,r-iranges)
4428 ("r-mapplots" ,r-mapplots)
4430 ("r-vioplot" ,r-vioplot)))
4432 `(("r-knitr" ,r-knitr)))
4433 (home-page "https://bioconductor.org/packages/GOfuncR/")
4434 (synopsis "Gene ontology enrichment using FUNC")
4436 "GOfuncR performs a gene ontology enrichment analysis based on the
4437 ontology enrichment software FUNC. GO-annotations are obtained from
4438 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
4439 included in the package and updated regularly. GOfuncR provides the standard
4440 candidate vs background enrichment analysis using the hypergeometric test, as
4441 well as three additional tests:
4444 @item the Wilcoxon rank-sum test that is used when genes are ranked,
4445 @item a binomial test that is used when genes are associated with two counts,
4447 @item a Chi-square or Fisher's exact test that is used in cases when genes are
4448 associated with four counts.
4451 To correct for multiple testing and interdependency of the tests, family-wise
4452 error rates are computed based on random permutations of the gene-associated
4453 variables. GOfuncR also provides tools for exploring the ontology graph and
4454 the annotations, and options to take gene-length or spatial clustering of
4455 genes into account. It is also possible to provide custom gene coordinates,
4456 annotations and ontologies.")
4457 (license license:gpl2+)))
4459 (define-public r-abaenrichment
4461 (name "r-abaenrichment")
4466 (uri (bioconductor-uri "ABAEnrichment" version))
4469 "09ihbgxrhpcz2q7svldhm710a0yrhiqk9p0q0myv11c2w50ymwkw"))))
4470 (properties `((upstream-name . "ABAEnrichment")))
4471 (build-system r-build-system)
4473 `(("r-abadata" ,r-abadata)
4474 ("r-data-table" ,r-data-table)
4475 ("r-gofuncr" ,r-gofuncr)
4476 ("r-gplots" ,r-gplots)
4477 ("r-gtools" ,r-gtools)
4478 ("r-rcpp" ,r-rcpp)))
4480 `(("r-knitr" ,r-knitr)))
4481 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4482 (synopsis "Gene expression enrichment in human brain regions")
4484 "The package ABAEnrichment is designed to test for enrichment of user
4485 defined candidate genes in the set of expressed genes in different human brain
4486 regions. The core function @code{aba_enrich} integrates the expression of the
4487 candidate gene set (averaged across donors) and the structural information of
4488 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4489 (license license:gpl2+)))
4491 (define-public r-annotationfuncs
4493 (name "r-annotationfuncs")
4498 (uri (bioconductor-uri "AnnotationFuncs" version))
4501 "1yfsxzn7s1nlc3xz2yj39j6hmdfapc9qj9h0cd71gkaxj53ial7d"))))
4503 `((upstream-name . "AnnotationFuncs")))
4504 (build-system r-build-system)
4506 `(("r-annotationdbi" ,r-annotationdbi)
4508 (home-page "https://www.iysik.com/r/annotationfuncs")
4509 (synopsis "Annotation translation functions")
4511 "This package provides functions for handling translating between
4512 different identifieres using the Biocore Data Team data-packages (e.g.
4513 @code{org.Bt.eg.db}).")
4514 (license license:gpl2)))
4516 (define-public r-annotationtools
4518 (name "r-annotationtools")
4523 (uri (bioconductor-uri "annotationTools" version))
4526 "1b1yfnknr9vbn4y2mxdfyx57i5jbabhp9pwx8axlg2a7lawkfmdk"))))
4528 `((upstream-name . "annotationTools")))
4529 (build-system r-build-system)
4530 (propagated-inputs `(("r-biobase" ,r-biobase)))
4531 (home-page "https://bioconductor.org/packages/annotationTools/")
4532 (synopsis "Annotate microarrays and perform gene expression analyses")
4534 "This package provides functions to annotate microarrays, find orthologs,
4535 and integrate heterogeneous gene expression profiles using annotation and
4536 other molecular biology information available as flat file database (plain
4538 ;; Any version of the GPL.
4539 (license (list license:gpl2+))))
4541 (define-public r-allelicimbalance
4543 (name "r-allelicimbalance")
4548 (uri (bioconductor-uri "AllelicImbalance" version))
4551 "0irn4xdlvazdkv0055f45693y6zvqaz7j3vml5xscnh45ls6vmqr"))))
4553 `((upstream-name . "AllelicImbalance")))
4554 (build-system r-build-system)
4556 `(("r-annotationdbi" ,r-annotationdbi)
4557 ("r-biocgenerics" ,r-biocgenerics)
4558 ("r-biostrings" ,r-biostrings)
4559 ("r-bsgenome" ,r-bsgenome)
4560 ("r-genomeinfodb" ,r-genomeinfodb)
4561 ("r-genomicalignments" ,r-genomicalignments)
4562 ("r-genomicfeatures" ,r-genomicfeatures)
4563 ("r-genomicranges" ,r-genomicranges)
4564 ("r-gridextra" ,r-gridextra)
4566 ("r-iranges" ,r-iranges)
4567 ("r-lattice" ,r-lattice)
4568 ("r-latticeextra" ,r-latticeextra)
4570 ("r-rsamtools" ,r-rsamtools)
4571 ("r-s4vectors" ,r-s4vectors)
4572 ("r-seqinr" ,r-seqinr)
4573 ("r-summarizedexperiment" ,r-summarizedexperiment)
4574 ("r-variantannotation" ,r-variantannotation)))
4576 `(("r-knitr" ,r-knitr)))
4577 (home-page "https://github.com/pappewaio/AllelicImbalance")
4578 (synopsis "Investigate allele-specific expression")
4580 "This package provides a framework for allele-specific expression
4581 investigation using RNA-seq data.")
4582 (license license:gpl3)))
4584 (define-public r-aucell
4591 (uri (bioconductor-uri "AUCell" version))
4594 "0fgqkgjhf92vkljkwn44lm8cjvzq1lvk80nk6xhsp5q6s5isbmns"))))
4595 (properties `((upstream-name . "AUCell")))
4596 (build-system r-build-system)
4598 `(("r-biocgenerics" ,r-biocgenerics)
4599 ("r-data-table" ,r-data-table)
4600 ("r-gseabase" ,r-gseabase)
4601 ("r-mixtools" ,r-mixtools)
4602 ("r-r-utils" ,r-r-utils)
4603 ("r-s4vectors" ,r-s4vectors)
4604 ("r-shiny" ,r-shiny)
4605 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4607 `(("r-knitr" ,r-knitr)))
4608 (home-page "https://bioconductor.org/packages/AUCell/")
4609 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4611 "AUCell identifies cells with active gene sets (e.g. signatures,
4612 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4613 Under the Curve} (AUC) to calculate whether a critical subset of the input
4614 gene set is enriched within the expressed genes for each cell. The
4615 distribution of AUC scores across all the cells allows exploring the relative
4616 expression of the signature. Since the scoring method is ranking-based,
4617 AUCell is independent of the gene expression units and the normalization
4618 procedure. In addition, since the cells are evaluated individually, it can
4619 easily be applied to bigger datasets, subsetting the expression matrix if
4621 (license license:gpl3)))
4623 (define-public r-ebimage
4630 (uri (bioconductor-uri "EBImage" version))
4633 "13amrbh545hwk7sygndzyv7wpa0m2y0lzlwj89jm1xm62x577w9v"))))
4634 (properties `((upstream-name . "EBImage")))
4635 (build-system r-build-system)
4637 `(("r-abind" ,r-abind)
4638 ("r-biocgenerics" ,r-biocgenerics)
4639 ("r-fftwtools" ,r-fftwtools)
4640 ("r-htmltools" ,r-htmltools)
4641 ("r-htmlwidgets" ,r-htmlwidgets)
4643 ("r-locfit" ,r-locfit)
4645 ("r-rcurl" ,r-rcurl)
4646 ("r-tiff" ,r-tiff)))
4648 `(("r-knitr" ,r-knitr))) ; for vignettes
4649 (home-page "https://github.com/aoles/EBImage")
4650 (synopsis "Image processing and analysis toolbox for R")
4652 "EBImage provides general purpose functionality for image processing and
4653 analysis. In the context of (high-throughput) microscopy-based cellular
4654 assays, EBImage offers tools to segment cells and extract quantitative
4655 cellular descriptors. This allows the automation of such tasks using the R
4656 programming language and facilitates the use of other tools in the R
4657 environment for signal processing, statistical modeling, machine learning and
4658 visualization with image data.")
4659 ;; Any version of the LGPL.
4660 (license license:lgpl2.1+)))
4662 (define-public r-yamss
4669 (uri (bioconductor-uri "yamss" version))
4672 "00x2lnssgzbmhy5bb2m0f8rq2nsz3lb5xlp2vhkcagza39h3xb0c"))))
4673 (build-system r-build-system)
4675 `(("r-biocgenerics" ,r-biocgenerics)
4676 ("r-data-table" ,r-data-table)
4677 ("r-ebimage" ,r-ebimage)
4678 ("r-iranges" ,r-iranges)
4679 ("r-limma" ,r-limma)
4680 ("r-matrix" ,r-matrix)
4682 ("r-s4vectors" ,r-s4vectors)
4683 ("r-summarizedexperiment"
4684 ,r-summarizedexperiment)))
4686 `(("r-knitr" ,r-knitr)))
4687 (home-page "https://github.com/hansenlab/yamss")
4688 (synopsis "Tools for high-throughput metabolomics")
4690 "This package provides tools to analyze and visualize high-throughput
4691 metabolomics data acquired using chromatography-mass spectrometry. These tools
4692 preprocess data in a way that enables reliable and powerful differential
4694 (license license:artistic2.0)))
4696 (define-public r-gtrellis
4703 (uri (bioconductor-uri "gtrellis" version))
4706 "1v2l7r945xx4cf9s8m19csj7716n2ayxy05adkl8zqgxk0gxzqm1"))))
4707 (build-system r-build-system)
4709 `(("r-circlize" ,r-circlize)
4710 ("r-genomicranges" ,r-genomicranges)
4711 ("r-getoptlong" ,r-getoptlong)
4712 ("r-iranges" ,r-iranges)))
4714 `(("r-knitr" ,r-knitr)))
4715 (home-page "https://github.com/jokergoo/gtrellis")
4716 (synopsis "Genome level Trellis layout")
4718 "Genome level Trellis graph visualizes genomic data conditioned by
4719 genomic categories (e.g. chromosomes). For each genomic category, multiple
4720 dimensional data which are represented as tracks describe different features
4721 from different aspects. This package provides high flexibility to arrange
4722 genomic categories and to add self-defined graphics in the plot.")
4723 (license license:expat)))
4725 (define-public r-somaticsignatures
4727 (name "r-somaticsignatures")
4732 (uri (bioconductor-uri "SomaticSignatures" version))
4735 "0d34mss73w1jdnmilk060a1fywlfmqbnlir089q9m3q1p3x0j4c1"))))
4737 `((upstream-name . "SomaticSignatures")))
4738 (build-system r-build-system)
4740 `(("r-biobase" ,r-biobase)
4741 ("r-biostrings" ,r-biostrings)
4742 ("r-genomeinfodb" ,r-genomeinfodb)
4743 ("r-genomicranges" ,r-genomicranges)
4744 ("r-ggbio" ,r-ggbio)
4745 ("r-ggplot2" ,r-ggplot2)
4746 ("r-iranges" ,r-iranges)
4748 ("r-pcamethods" ,r-pcamethods)
4749 ("r-proxy" ,r-proxy)
4750 ("r-reshape2" ,r-reshape2)
4751 ("r-s4vectors" ,r-s4vectors)
4752 ("r-variantannotation" ,r-variantannotation)))
4754 `(("r-knitr" ,r-knitr)))
4755 (home-page "https://github.com/juliangehring/SomaticSignatures")
4756 (synopsis "Somatic signatures")
4758 "This package identifies mutational signatures of @dfn{single nucleotide
4759 variants} (SNVs). It provides a infrastructure related to the methodology
4760 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4761 decomposition algorithms.")
4762 (license license:expat)))
4764 (define-public r-yapsa
4771 (uri (bioconductor-uri "YAPSA" version))
4774 "06lkf01vl4fyhj82srx8k870fhw76a1han0kp4jglh43b1c19c1k"))))
4775 (properties `((upstream-name . "YAPSA")))
4776 (build-system r-build-system)
4778 `(("r-biostrings" ,r-biostrings)
4779 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
4780 ("r-circlize" ,r-circlize)
4781 ("r-complexheatmap" ,r-complexheatmap)
4782 ("r-corrplot" ,r-corrplot)
4783 ("r-dendextend" ,r-dendextend)
4784 ("r-doparallel" ,r-doparallel)
4785 ("r-dplyr" ,r-dplyr)
4786 ("r-genomeinfodb" ,r-genomeinfodb)
4787 ("r-genomicranges" ,r-genomicranges)
4788 ("r-getoptlong" ,r-getoptlong)
4789 ("r-ggbeeswarm" ,r-ggbeeswarm)
4790 ("r-ggplot2" ,r-ggplot2)
4791 ("r-gridextra" ,r-gridextra)
4792 ("r-gtrellis" ,r-gtrellis)
4793 ("r-keggrest" ,r-keggrest)
4795 ("r-magrittr" ,r-magrittr)
4796 ("r-pmcmr" ,r-pmcmr)
4797 ("r-pracma" ,r-pracma)
4798 ("r-reshape2" ,r-reshape2)
4799 ("r-somaticsignatures" ,r-somaticsignatures)
4800 ("r-variantannotation" ,r-variantannotation)))
4802 `(("r-knitr" ,r-knitr)))
4803 (home-page "https://bioconductor.org/packages/YAPSA/")
4804 (synopsis "Yet another package for signature analysis")
4806 "This package provides functions and routines useful in the analysis of
4807 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4808 functions to perform a signature analysis with known signatures and a
4809 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4811 (license license:gpl3)))
4813 (define-public r-gcrma
4820 (uri (bioconductor-uri "gcrma" version))
4823 "1klbnygc1i5ac1x00bsk0rjw5h5dn6pn65fa3y9r09q47gpy1c5g"))))
4824 (build-system r-build-system)
4826 `(("r-affy" ,r-affy)
4827 ("r-affyio" ,r-affyio)
4828 ("r-biobase" ,r-biobase)
4829 ("r-biocmanager" ,r-biocmanager)
4830 ("r-biostrings" ,r-biostrings)
4831 ("r-xvector" ,r-xvector)))
4832 (home-page "https://bioconductor.org/packages/gcrma/")
4833 (synopsis "Background adjustment using sequence information")
4835 "Gcrma adjusts for background intensities in Affymetrix array data which
4836 include optical noise and @dfn{non-specific binding} (NSB). The main function
4837 @code{gcrma} converts background adjusted probe intensities to expression
4838 measures using the same normalization and summarization methods as a
4839 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4840 to estimate probe affinity to NSB. The sequence information is summarized in
4841 a more complex way than the simple GC content. Instead, the base types (A, T,
4842 G or C) at each position along the probe determine the affinity of each probe.
4843 The parameters of the position-specific base contributions to the probe
4844 affinity is estimated in an NSB experiment in which only NSB but no
4845 gene-specific bidning is expected.")
4846 ;; Any version of the LGPL
4847 (license license:lgpl2.1+)))
4849 (define-public r-simpleaffy
4851 (name "r-simpleaffy")
4856 (uri (bioconductor-uri "simpleaffy" version))
4859 "040043spblr8v67lkn3nnxhgfmfh2iwaizph4fnms1ik6qz662x7"))))
4860 (build-system r-build-system)
4862 `(("r-affy" ,r-affy)
4863 ("r-biobase" ,r-biobase)
4864 ("r-biocgenerics" ,r-biocgenerics)
4865 ("r-gcrma" ,r-gcrma)
4866 ("r-genefilter" ,r-genefilter)))
4867 (home-page "https://bioconductor.org/packages/simpleaffy/")
4868 (synopsis "Very simple high level analysis of Affymetrix data")
4870 "This package provides high level functions for reading Affy @file{.CEL}
4871 files, phenotypic data, and then computing simple things with it, such as
4872 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4873 library. It also has some basic scatter plot functions and mechanisms for
4874 generating high resolution journal figures.")
4875 (license license:gpl2+)))
4877 (define-public r-yaqcaffy
4884 (uri (bioconductor-uri "yaqcaffy" version))
4887 "1l0cblh9sfrsil15bjya7d8kkas8bj6klj2w3c4384njdsjsjcf0"))))
4888 (build-system r-build-system)
4890 `(("r-simpleaffy" ,r-simpleaffy)))
4891 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4892 (synopsis "Affymetrix quality control and reproducibility analysis")
4894 "This is a package that can be used for quality control of Affymetrix
4895 GeneChip expression data and reproducibility analysis of human whole genome
4896 chips with the MAQC reference datasets.")
4897 (license license:artistic2.0)))
4899 (define-public r-quantro
4906 (uri (bioconductor-uri "quantro" version))
4909 "0ap9cl5z79wg44mnagjsk8py3kngb4f0ddnx85cbnwqkvb769zbz"))))
4910 (build-system r-build-system)
4912 `(("r-biobase" ,r-biobase)
4913 ("r-doparallel" ,r-doparallel)
4914 ("r-foreach" ,r-foreach)
4915 ("r-ggplot2" ,r-ggplot2)
4916 ("r-iterators" ,r-iterators)
4917 ("r-minfi" ,r-minfi)
4918 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4920 `(("r-knitr" ,r-knitr)))
4921 (home-page "https://bioconductor.org/packages/quantro/")
4922 (synopsis "Test for when to use quantile normalization")
4924 "This package provides a data-driven test for the assumptions of quantile
4925 normalization using raw data such as objects that inherit eSets (e.g.
4926 ExpressionSet, MethylSet). Group level information about each sample (such as
4927 Tumor / Normal status) must also be provided because the test assesses if
4928 there are global differences in the distributions between the user-defined
4930 (license license:gpl3+)))
4932 (define-public r-yarn
4939 (uri (bioconductor-uri "yarn" version))
4942 "1xdjwy1gkfg8lhgq4iwwmbi01903qljjs7yd96cvacmvgn8z6qvx"))))
4943 (build-system r-build-system)
4945 `(("r-biobase" ,r-biobase)
4946 ("r-biomart" ,r-biomart)
4947 ("r-downloader" ,r-downloader)
4948 ("r-edger" ,r-edger)
4949 ("r-gplots" ,r-gplots)
4950 ("r-limma" ,r-limma)
4951 ("r-matrixstats" ,r-matrixstats)
4952 ("r-preprocesscore" ,r-preprocesscore)
4953 ("r-quantro" ,r-quantro)
4954 ("r-rcolorbrewer" ,r-rcolorbrewer)
4955 ("r-readr" ,r-readr)))
4957 `(("r-knitr" ,r-knitr)))
4958 (home-page "https://bioconductor.org/packages/yarn/")
4959 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4961 "Expedite large RNA-Seq analyses using a combination of previously
4962 developed tools. YARN is meant to make it easier for the user in performing
4963 basic mis-annotation quality control, filtering, and condition-aware
4964 normalization. YARN leverages many Bioconductor tools and statistical
4965 techniques to account for the large heterogeneity and sparsity found in very
4966 large RNA-seq experiments.")
4967 (license license:artistic2.0)))
4969 (define-public r-roar
4976 (uri (bioconductor-uri "roar" version))
4979 "069g887migvk70n0377dqr0fk7wjbz3w0asgk42bwhp8xpjfym6f"))))
4980 (build-system r-build-system)
4982 `(("r-biocgenerics" ,r-biocgenerics)
4983 ("r-genomeinfodb" ,r-genomeinfodb)
4984 ("r-genomicalignments" ,r-genomicalignments)
4985 ("r-genomicranges" ,r-genomicranges)
4986 ("r-iranges" ,r-iranges)
4987 ("r-rtracklayer" ,r-rtracklayer)
4988 ("r-s4vectors" ,r-s4vectors)
4989 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4990 (home-page "https://github.com/vodkatad/roar/")
4991 (synopsis "Identify differential APA usage from RNA-seq alignments")
4993 "This package provides tools for identifying preferential usage of APA
4994 sites, comparing two biological conditions, starting from known alternative
4995 sites and alignments obtained from standard RNA-seq experiments.")
4996 (license license:gpl3)))
4998 (define-public r-xbseq
5005 (uri (bioconductor-uri "XBSeq" version))
5008 "13br7x1q6dg8daxahskwq24f09wbxr8kyszl1z7dhc26bid2pvy0"))))
5009 (properties `((upstream-name . "XBSeq")))
5010 (build-system r-build-system)
5012 `(("r-biobase" ,r-biobase)
5013 ("r-deseq2" ,r-deseq2)
5014 ("r-dplyr" ,r-dplyr)
5015 ("r-ggplot2" ,r-ggplot2)
5016 ("r-locfit" ,r-locfit)
5017 ("r-magrittr" ,r-magrittr)
5018 ("r-matrixstats" ,r-matrixstats)
5019 ("r-pracma" ,r-pracma)
5020 ("r-roar" ,r-roar)))
5022 `(("r-knitr" ,r-knitr)))
5023 (home-page "https://github.com/Liuy12/XBSeq")
5024 (synopsis "Test for differential expression for RNA-seq data")
5026 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
5027 expression} (DE), where a statistical model was established based on the
5028 assumption that observed signals are the convolution of true expression
5029 signals and sequencing noises. The mapped reads in non-exonic regions are
5030 considered as sequencing noises, which follows a Poisson distribution. Given
5031 measurable observed signal and background noise from RNA-seq data, true
5032 expression signals, assuming governed by the negative binomial distribution,
5033 can be delineated and thus the accurate detection of differential expressed
5035 (license license:gpl3+)))
5037 (define-public r-massspecwavelet
5039 (name "r-massspecwavelet")
5044 (uri (bioconductor-uri "MassSpecWavelet" version))
5047 "0nv1r68g7f1rps6sqaccd4n4x0i19wklvyabhp4b03cdk22gl3nq"))))
5049 `((upstream-name . "MassSpecWavelet")))
5050 (build-system r-build-system)
5052 `(("r-waveslim" ,r-waveslim)))
5053 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
5054 (synopsis "Mass spectrum processing by wavelet-based algorithms")
5056 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
5057 data mainly through the use of wavelet transforms. It supports peak detection
5058 based on @dfn{Continuous Wavelet Transform} (CWT).")
5059 (license license:lgpl2.0+)))
5061 (define-public r-xcms
5068 (uri (bioconductor-uri "xcms" version))
5071 "1aa11gy1v7kkamv3hsnvdx715q8f1saw9p664j6wifyjj0hx13kn"))))
5072 (build-system r-build-system)
5074 `(("r-biobase" ,r-biobase)
5075 ("r-biocgenerics" ,r-biocgenerics)
5076 ("r-biocparallel" ,r-biocparallel)
5077 ("r-iranges" ,r-iranges)
5078 ("r-lattice" ,r-lattice)
5079 ("r-massspecwavelet" ,r-massspecwavelet)
5080 ("r-msnbase" ,r-msnbase)
5083 ("r-protgenerics" ,r-protgenerics)
5085 ("r-rcolorbrewer" ,r-rcolorbrewer)
5086 ("r-robustbase" ,r-robustbase)
5087 ("r-s4vectors" ,r-s4vectors)
5088 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5090 `(("r-knitr" ,r-knitr)))
5091 (home-page "https://bioconductor.org/packages/xcms/")
5092 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
5094 "This package provides a framework for processing and visualization of
5095 chromatographically separated and single-spectra mass spectral data. It
5096 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
5097 data for high-throughput, untargeted analyte profiling.")
5098 (license license:gpl2+)))
5100 (define-public r-wrench
5107 (uri (bioconductor-uri "Wrench" version))
5110 "05dyk3yvbqrzvinv3ig8ad9wffwr14z715cicsbxwxpv5lq84wx6"))))
5111 (properties `((upstream-name . "Wrench")))
5112 (build-system r-build-system)
5114 `(("r-limma" ,r-limma)
5115 ("r-locfit" ,r-locfit)
5116 ("r-matrixstats" ,r-matrixstats)))
5118 `(("r-knitr" ,r-knitr)))
5119 (home-page "https://github.com/HCBravoLab/Wrench")
5120 (synopsis "Wrench normalization for sparse count data")
5122 "Wrench is a package for normalization sparse genomic count data, like
5123 that arising from 16s metagenomic surveys.")
5124 (license license:artistic2.0)))
5126 (define-public r-wiggleplotr
5128 (name "r-wiggleplotr")
5133 (uri (bioconductor-uri "wiggleplotr" version))
5136 "1wknigh1md3w4h68caqlpq945maipdkpmw10hc2rlx4nbbpcnawp"))))
5137 (build-system r-build-system)
5139 `(("r-assertthat" ,r-assertthat)
5140 ("r-cowplot" ,r-cowplot)
5141 ("r-dplyr" ,r-dplyr)
5142 ("r-genomeinfodb" ,r-genomeinfodb)
5143 ("r-genomicranges" ,r-genomicranges)
5144 ("r-ggplot2" ,r-ggplot2)
5145 ("r-iranges" ,r-iranges)
5146 ("r-purrr" ,r-purrr)
5147 ("r-rtracklayer" ,r-rtracklayer)
5148 ("r-s4vectors" ,r-s4vectors)))
5150 `(("r-knitr" ,r-knitr)))
5151 (home-page "https://bioconductor.org/packages/wiggleplotr/")
5152 (synopsis "Make read coverage plots from BigWig files")
5154 "This package provides tools to visualize read coverage from sequencing
5155 experiments together with genomic annotations (genes, transcripts, peaks).
5156 Introns of long transcripts can be rescaled to a fixed length for better
5157 visualization of exonic read coverage.")
5158 (license license:asl2.0)))
5160 (define-public r-widgettools
5162 (name "r-widgettools")
5167 (uri (bioconductor-uri "widgetTools" version))
5170 "0lrdpsgm9r7yfyyj5crvb7px4hrghxhmiic4iissz40slbfyvilx"))))
5171 (properties `((upstream-name . "widgetTools")))
5172 (build-system r-build-system)
5173 (home-page "https://bioconductor.org/packages/widgetTools/")
5174 (synopsis "Tools for creating interactive tcltk widgets")
5176 "This package contains tools to support the construction of tcltk
5178 ;; Any version of the LGPL.
5179 (license license:lgpl3+)))
5181 (define-public r-webbioc
5188 (uri (bioconductor-uri "webbioc" version))
5191 "16376ya5a5x2hwkl1v9y4r7np1drdwm912knnqg2dn90zmrdwr5f"))))
5192 (build-system r-build-system)
5194 `(("netpbm" ,netpbm)
5197 `(("r-affy" ,r-affy)
5198 ("r-annaffy" ,r-annaffy)
5199 ("r-biobase" ,r-biobase)
5200 ("r-biocmanager" ,r-biocmanager)
5201 ("r-gcrma" ,r-gcrma)
5202 ("r-multtest" ,r-multtest)
5203 ("r-qvalue" ,r-qvalue)
5205 (home-page "https://www.bioconductor.org/")
5206 (synopsis "Bioconductor web interface")
5208 "This package provides an integrated web interface for doing microarray
5209 analysis using several of the Bioconductor packages. It is intended to be
5210 deployed as a centralized bioinformatics resource for use by many users.
5211 Currently only Affymetrix oligonucleotide analysis is supported.")
5212 (license license:gpl2+)))
5214 (define-public r-zfpkm
5221 (uri (bioconductor-uri "zFPKM" version))
5224 "0scszhfqrgzhglz1a6kxfydq9dx8fqx28j3dypp91y5ah2w6mdys"))))
5225 (properties `((upstream-name . "zFPKM")))
5226 (build-system r-build-system)
5228 `(("r-checkmate" ,r-checkmate)
5229 ("r-dplyr" ,r-dplyr)
5230 ("r-ggplot2" ,r-ggplot2)
5231 ("r-summarizedexperiment" ,r-summarizedexperiment)
5232 ("r-tidyr" ,r-tidyr)))
5234 `(("r-knitr" ,r-knitr)))
5235 (home-page "https://github.com/ronammar/zFPKM/")
5236 (synopsis "Functions to facilitate zFPKM transformations")
5238 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
5239 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
5241 (license license:gpl3)))
5243 (define-public r-rbowtie2
5250 (uri (bioconductor-uri "Rbowtie2" version))
5253 "19v7wfvrd53j618c1xbiqnlsf2kxw697myryx0vb9s2aspknyzz7"))))
5254 (properties `((upstream-name . "Rbowtie2")))
5255 (build-system r-build-system)
5259 `(("r-knitr" ,r-knitr)))
5260 (home-page "https://bioconductor.org/packages/Rbowtie2/")
5261 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
5263 "This package provides an R wrapper of the popular @code{bowtie2}
5264 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
5265 rapid adapter trimming, identification, and read merging.")
5266 (license license:gpl3+)))
5268 (define-public r-progeny
5275 (uri (bioconductor-uri "progeny" version))
5278 "09rq3nf9zm7w9djmx8xc8j3win3597p2v36zqgkhgkjwq5rkjgsh"))))
5279 (build-system r-build-system)
5281 `(("r-biobase" ,r-biobase)
5282 ("r-dplyr" ,r-dplyr)
5283 ("r-ggplot2" ,r-ggplot2)
5284 ("r-ggrepel" ,r-ggrepel)
5285 ("r-gridextra" ,r-gridextra)
5286 ("r-tidyr" ,r-tidyr)))
5288 `(("r-knitr" ,r-knitr)))
5289 (home-page "https://github.com/saezlab/progeny")
5290 (synopsis "Pathway responsive gene activity inference")
5292 "This package provides a function to infer pathway activity from gene
5293 expression. It contains the linear model inferred in the publication
5294 \"Perturbation-response genes reveal signaling footprints in cancer gene
5296 (license license:asl2.0)))
5298 (define-public r-arrmnormalization
5300 (name "r-arrmnormalization")
5305 (uri (bioconductor-uri "ARRmNormalization" version))
5308 "0zhhvr051fmh6g0bqrl525mkf094j1jnc57j201jlzmvdpkydlpv"))))
5310 `((upstream-name . "ARRmNormalization")))
5311 (build-system r-build-system)
5312 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
5313 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
5314 (synopsis "Adaptive robust regression normalization for methylation data")
5316 "This is a package to perform the @dfn{Adaptive Robust Regression
5317 method} (ARRm) for the normalization of methylation data from the Illumina
5318 Infinium HumanMethylation 450k assay.")
5319 (license license:artistic2.0)))
5321 (define-public r-biocfilecache
5323 (name "r-biocfilecache")
5328 (uri (bioconductor-uri "BiocFileCache" version))
5331 "02yayjyliaqxcwqa0n2ccmsfflskqzf0gvdibh2r3nz5bi66imkf"))))
5332 (properties `((upstream-name . "BiocFileCache")))
5333 (build-system r-build-system)
5335 `(("r-curl" ,r-curl)
5337 ("r-dbplyr" ,r-dbplyr)
5338 ("r-dplyr" ,r-dplyr)
5340 ("r-rappdirs" ,r-rappdirs)
5341 ("r-rsqlite" ,r-rsqlite)))
5343 `(("r-knitr" ,r-knitr)))
5344 (home-page "https://bioconductor.org/packages/BiocFileCache/")
5345 (synopsis "Manage files across sessions")
5347 "This package creates a persistent on-disk cache of files that the user
5348 can add, update, and retrieve. It is useful for managing resources (such as
5349 custom Txdb objects) that are costly or difficult to create, web resources,
5350 and data files used across sessions.")
5351 (license license:artistic2.0)))
5353 (define-public r-iclusterplus
5355 (name "r-iclusterplus")
5360 (uri (bioconductor-uri "iClusterPlus" version))
5363 "0j987xvxixdz0wnhgp4kgfcgz5jffrcdhmldrgpgv582qmf4r94w"))))
5364 (properties `((upstream-name . "iClusterPlus")))
5365 (build-system r-build-system)
5366 (native-inputs `(("gfortran" ,gfortran)))
5367 (home-page "https://bioconductor.org/packages/iClusterPlus/")
5368 (synopsis "Integrative clustering of multi-type genomic data")
5370 "iClusterPlus is developed for integrative clustering analysis of
5371 multi-type genomic data and is an enhanced version of iCluster proposed and
5372 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
5373 from the experiments where biological samples (e.g. tumor samples) are
5374 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
5375 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
5376 on. In the iClusterPlus model, binary observations such as somatic mutation
5377 are modeled as Binomial processes; categorical observations such as copy
5378 number states are realizations of Multinomial random variables; counts are
5379 modeled as Poisson random processes; and continuous measures are modeled by
5380 Gaussian distributions.")
5381 (license license:gpl2+)))
5383 (define-public r-rbowtie
5390 (uri (bioconductor-uri "Rbowtie" version))
5393 "0589ggbfx6di42wvqyhnzgrhmb52swr3r5z22w6b8x0z2y7hl8b3"))))
5394 (properties `((upstream-name . "Rbowtie")))
5395 (build-system r-build-system)
5399 `(("r-knitr" ,r-knitr)))
5400 (home-page "https://bioconductor.org/packages/Rbowtie/")
5401 (synopsis "R bowtie wrapper")
5403 "This package provides an R wrapper around the popular bowtie short read
5404 aligner and around SpliceMap, a de novo splice junction discovery and
5406 (license license:artistic2.0)))
5408 (define-public r-sgseq
5415 (uri (bioconductor-uri "SGSeq" version))
5418 "11rxx7abjyga2sdcp4x4z3n8xjx6973sckyzmh9ax6r46kwhxq8c"))))
5419 (properties `((upstream-name . "SGSeq")))
5420 (build-system r-build-system)
5422 `(("r-annotationdbi" ,r-annotationdbi)
5423 ("r-biocgenerics" ,r-biocgenerics)
5424 ("r-biostrings" ,r-biostrings)
5425 ("r-genomeinfodb" ,r-genomeinfodb)
5426 ("r-genomicalignments" ,r-genomicalignments)
5427 ("r-genomicfeatures" ,r-genomicfeatures)
5428 ("r-genomicranges" ,r-genomicranges)
5429 ("r-igraph" ,r-igraph)
5430 ("r-iranges" ,r-iranges)
5431 ("r-rsamtools" ,r-rsamtools)
5432 ("r-rtracklayer" ,r-rtracklayer)
5433 ("r-runit" ,r-runit)
5434 ("r-s4vectors" ,r-s4vectors)
5435 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5437 `(("r-knitr" ,r-knitr)))
5438 (home-page "https://bioconductor.org/packages/SGSeq/")
5439 (synopsis "Splice event prediction and quantification from RNA-seq data")
5441 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
5442 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
5443 represented as a splice graph, which can be obtained from existing annotation
5444 or predicted from the mapped sequence reads. Splice events are identified
5445 from the graph and are quantified locally using structurally compatible reads
5446 at the start or end of each splice variant. The software includes functions
5447 for splice event prediction, quantification, visualization and
5449 (license license:artistic2.0)))
5451 (define-public r-rhisat2
5458 (uri (bioconductor-uri "Rhisat2" version))
5461 "0hhmcdnixkaqx9x9cl2vjaba3ri8m6wkbnbhxjmy51jwqzy2223a"))))
5462 (properties `((upstream-name . "Rhisat2")))
5463 (build-system r-build-system)
5466 (modify-phases %standard-phases
5467 (add-after 'unpack 'make-reproducible
5469 (substitute* "src/Makefile"
5470 (("`hostname`") "guix")
5472 ;; Avoid shelling out to "which".
5473 (("^CC =.*") (which "gcc"))
5474 (("^CPP =.*") (which "g++")))
5477 `(("r-genomicfeatures" ,r-genomicfeatures)
5478 ("r-genomicranges" ,r-genomicranges)
5479 ("r-sgseq" ,r-sgseq)))
5481 `(("r-knitr" ,r-knitr)))
5482 (home-page "https://github.com/fmicompbio/Rhisat2")
5483 (synopsis "R Wrapper for HISAT2 sequence aligner")
5485 "This package provides an R interface to the HISAT2 spliced short-read
5486 aligner by Kim et al. (2015). The package contains wrapper functions to
5487 create a genome index and to perform the read alignment to the generated
5489 (license license:gpl3)))
5491 (define-public r-quasr
5498 (uri (bioconductor-uri "QuasR" version))
5501 "0d87ajaaq8a7xgzl820qx5bvxw86ppab8clqk77sj02rfijnvjn8"))))
5502 (properties `((upstream-name . "QuasR")))
5503 (build-system r-build-system)
5507 `(("r-annotationdbi" ,r-annotationdbi)
5508 ("r-biobase" ,r-biobase)
5509 ("r-biocgenerics" ,r-biocgenerics)
5510 ("r-biocmanager" ,r-biocmanager)
5511 ("r-biocparallel" ,r-biocparallel)
5512 ("r-biostrings" ,r-biostrings)
5513 ("r-bsgenome" ,r-bsgenome)
5514 ("r-genomeinfodb" ,r-genomeinfodb)
5515 ("r-genomicalignments" ,r-genomicalignments)
5516 ("r-genomicfeatures" ,r-genomicfeatures)
5517 ("r-genomicfiles" ,r-genomicfiles)
5518 ("r-genomicranges" ,r-genomicranges)
5519 ("r-iranges" ,r-iranges)
5520 ("r-rbowtie" ,r-rbowtie)
5521 ("r-rhisat2" ,r-rhisat2)
5522 ("r-rhtslib" ,r-rhtslib)
5523 ("r-rsamtools" ,r-rsamtools)
5524 ("r-rtracklayer" ,r-rtracklayer)
5525 ("r-s4vectors" ,r-s4vectors)
5526 ("r-shortread" ,r-shortread)))
5528 `(("r-knitr" ,r-knitr)))
5529 (home-page "https://bioconductor.org/packages/QuasR/")
5530 (synopsis "Quantify and annotate short reads in R")
5532 "This package provides a framework for the quantification and analysis of
5533 short genomic reads. It covers a complete workflow starting from raw sequence
5534 reads, over creation of alignments and quality control plots, to the
5535 quantification of genomic regions of interest.")
5536 (license license:gpl2)))
5538 (define-public r-rqc
5545 (uri (bioconductor-uri "Rqc" version))
5548 "1qsm9r6xfsplk8zpf7p0k7fi86l8a74nx963sna8gzig5qgrvnm3"))))
5549 (properties `((upstream-name . "Rqc")))
5550 (build-system r-build-system)
5552 `(("r-biocgenerics" ,r-biocgenerics)
5553 ("r-biocparallel" ,r-biocparallel)
5554 ("r-biocstyle" ,r-biocstyle)
5555 ("r-biostrings" ,r-biostrings)
5556 ("r-biovizbase" ,r-biovizbase)
5557 ("r-genomicalignments" ,r-genomicalignments)
5558 ("r-genomicfiles" ,r-genomicfiles)
5559 ("r-ggplot2" ,r-ggplot2)
5560 ("r-iranges" ,r-iranges)
5561 ("r-knitr" ,r-knitr)
5562 ("r-markdown" ,r-markdown)
5565 ("r-reshape2" ,r-reshape2)
5566 ("r-rsamtools" ,r-rsamtools)
5567 ("r-s4vectors" ,r-s4vectors)
5568 ("r-shiny" ,r-shiny)
5569 ("r-shortread" ,r-shortread)))
5571 `(("r-knitr" ,r-knitr)))
5572 (home-page "https://github.com/labbcb/Rqc")
5573 (synopsis "Quality control tool for high-throughput sequencing data")
5575 "Rqc is an optimized tool designed for quality control and assessment of
5576 high-throughput sequencing data. It performs parallel processing of entire
5577 files and produces a report which contains a set of high-resolution
5579 (license license:gpl2+)))
5581 (define-public r-birewire
5588 (uri (bioconductor-uri "BiRewire" version))
5591 "0y7jb1abnik2y4ivpyqrgfl77rml6fhz88isd54l646ghslwxj0g"))))
5592 (properties `((upstream-name . "BiRewire")))
5593 (build-system r-build-system)
5595 `(("r-igraph" ,r-igraph)
5596 ("r-matrix" ,r-matrix)
5598 ("r-tsne" ,r-tsne)))
5599 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5600 (synopsis "Tools for randomization of bipartite graphs")
5602 "This package provides functions for bipartite network rewiring through N
5603 consecutive switching steps and for the computation of the minimal number of
5604 switching steps to be performed in order to maximise the dissimilarity with
5605 respect to the original network. It includes functions for the analysis of
5606 the introduced randomness across the switching steps and several other
5607 routines to analyse the resulting networks and their natural projections.")
5608 (license license:gpl3)))
5610 (define-public r-birta
5617 (uri (bioconductor-uri "birta" version))
5620 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
5621 (build-system r-build-system)
5623 `(("r-biobase" ,r-biobase)
5624 ("r-limma" ,r-limma)
5625 ("r-mass" ,r-mass)))
5626 (home-page "https://bioconductor.org/packages/birta")
5627 (synopsis "Bayesian inference of regulation of transcriptional activity")
5629 "Expression levels of mRNA molecules are regulated by different
5630 processes, comprising inhibition or activation by transcription factors and
5631 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5632 Inference of Regulation of Transcriptional Activity) uses the regulatory
5633 networks of transcription factors and miRNAs together with mRNA and miRNA
5634 expression data to predict switches in regulatory activity between two
5635 conditions. A Bayesian network is used to model the regulatory structure and
5636 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5637 (license license:gpl2+)))
5639 (define-public r-multidataset
5641 (name "r-multidataset")
5646 (uri (bioconductor-uri "MultiDataSet" version))
5649 "0hjnj32m9wwlh2krdpdyl5jk1cakvlgki80z51mabhc62pajzf39"))))
5650 (properties `((upstream-name . "MultiDataSet")))
5651 (build-system r-build-system)
5653 `(("r-biobase" ,r-biobase)
5654 ("r-biocgenerics" ,r-biocgenerics)
5655 ("r-genomicranges" ,r-genomicranges)
5656 ("r-ggplot2" ,r-ggplot2)
5657 ("r-ggrepel" ,r-ggrepel)
5658 ("r-iranges" ,r-iranges)
5659 ("r-limma" ,r-limma)
5660 ("r-qqman" ,r-qqman)
5661 ("r-s4vectors" ,r-s4vectors)
5662 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5664 `(("r-knitr" ,r-knitr)))
5665 (home-page "https://bioconductor.org/packages/MultiDataSet/")
5666 (synopsis "Implementation of MultiDataSet and ResultSet")
5668 "This package provides an implementation of the BRGE's (Bioinformatic
5669 Research Group in Epidemiology from Center for Research in Environmental
5670 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
5671 integrating multi omics data sets and ResultSet is a container for omics
5672 results. This package contains base classes for MEAL and rexposome
5674 (license license:expat)))
5676 (define-public r-ropls
5683 (uri (bioconductor-uri "ropls" version))
5686 "1drww1mr0nira3qplyga6s3mljpjxshjgbn524kzxi0nrfbcvmnx"))))
5687 (build-system r-build-system)
5689 `(("r-biobase" ,r-biobase)
5690 ("r-multidataset" ,r-multidataset)))
5692 `(("r-knitr" ,r-knitr))) ; for vignettes
5693 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5694 (synopsis "Multivariate analysis and feature selection of omics data")
5696 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5697 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5698 regression, classification, and feature selection of omics data where the
5699 number of variables exceeds the number of samples and with multicollinearity
5700 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5701 separately model the variation correlated (predictive) to the factor of
5702 interest and the uncorrelated (orthogonal) variation. While performing
5703 similarly to PLS, OPLS facilitates interpretation.
5705 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5706 analysis and feature selection of omics data. In addition to scores, loadings
5707 and weights plots, the package provides metrics and graphics to determine the
5708 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5709 validity of the model by permutation testing, detect outliers, and perform
5710 feature selection (e.g. with Variable Importance in Projection or regression
5712 (license license:cecill)))
5714 (define-public r-biosigner
5716 (name "r-biosigner")
5721 (uri (bioconductor-uri "biosigner" version))
5724 "1v760q7hzaybkf2q9230rmr4phi8hglm59qwsjzvncxrhs3dpj06"))))
5725 (build-system r-build-system)
5727 `(("r-biobase" ,r-biobase)
5728 ("r-e1071" ,r-e1071)
5729 ("r-multidataset" ,r-multidataset)
5730 ("r-randomforest" ,r-randomforest)
5731 ("r-ropls" ,r-ropls)))
5733 `(("r-knitr" ,r-knitr)))
5734 (home-page "https://bioconductor.org/packages/biosigner/")
5735 (synopsis "Signature discovery from omics data")
5737 "Feature selection is critical in omics data analysis to extract
5738 restricted and meaningful molecular signatures from complex and high-dimension
5739 data, and to build robust classifiers. This package implements a method to
5740 assess the relevance of the variables for the prediction performances of the
5741 classifier. The approach can be run in parallel with the PLS-DA, Random
5742 Forest, and SVM binary classifiers. The signatures and the corresponding
5743 'restricted' models are returned, enabling future predictions on new
5745 (license license:cecill)))
5747 (define-public r-annotatr
5754 (uri (bioconductor-uri "annotatr" version))
5757 "0z3ydcybd81w543fw8fiblghndx5m28w8qsphh5vqj726i0nj8cl"))))
5758 (build-system r-build-system)
5760 `(("r-annotationdbi" ,r-annotationdbi)
5761 ("r-annotationhub" ,r-annotationhub)
5762 ("r-dplyr" ,r-dplyr)
5763 ("r-genomeinfodb" ,r-genomeinfodb)
5764 ("r-genomicfeatures" ,r-genomicfeatures)
5765 ("r-genomicranges" ,r-genomicranges)
5766 ("r-ggplot2" ,r-ggplot2)
5767 ("r-iranges" ,r-iranges)
5768 ("r-readr" ,r-readr)
5769 ("r-regioner" ,r-regioner)
5770 ("r-reshape2" ,r-reshape2)
5771 ("r-rtracklayer" ,r-rtracklayer)
5772 ("r-s4vectors" ,r-s4vectors)))
5774 `(("r-knitr" ,r-knitr)))
5775 (home-page "https://bioconductor.org/packages/annotatr/")
5776 (synopsis "Annotation of genomic regions to genomic annotations")
5778 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5779 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5780 to investigate the intersecting genomic annotations. Such annotations include
5781 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5782 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5783 enhancers. The annotatr package provides an easy way to summarize and
5784 visualize the intersection of genomic sites/regions with genomic
5786 (license license:gpl3)))
5788 (define-public r-rsubread
5795 (uri (bioconductor-uri "Rsubread" version))
5798 "04h79qhq93d8id0rr5xnj9vf82ygwxzdlnck78yv738xd0jjvnpm"))))
5799 (properties `((upstream-name . "Rsubread")))
5800 (build-system r-build-system)
5801 (inputs `(("zlib" ,zlib)))
5803 `(("r-matrix" ,r-matrix)))
5804 (home-page "https://bioconductor.org/packages/Rsubread/")
5805 (synopsis "Subread sequence alignment and counting for R")
5807 "This package provides tools for alignment, quantification and analysis
5808 of second and third generation sequencing data. It includes functionality for
5809 read mapping, read counting, SNP calling, structural variant detection and
5810 gene fusion discovery. It can be applied to all major sequencing techologies
5811 and to both short and long sequence reads.")
5812 (license license:gpl3)))
5814 (define-public r-flowutils
5816 (name "r-flowutils")
5821 (uri (bioconductor-uri "flowUtils" version))
5824 "03jj4zyffm9kwzrg4vbsk6clc2v2m95wgalgqwzi31n9a2zyaza4"))))
5825 (properties `((upstream-name . "flowUtils")))
5826 (build-system r-build-system)
5828 `(("r-biobase" ,r-biobase)
5829 ("r-corpcor" ,r-corpcor)
5830 ("r-flowcore" ,r-flowcore)
5831 ("r-graph" ,r-graph)
5832 ("r-runit" ,r-runit)
5834 (home-page "https://github.com/jspidlen/flowUtils")
5835 (synopsis "Utilities for flow cytometry")
5837 "This package provides utilities for flow cytometry data.")
5838 (license license:artistic2.0)))
5840 (define-public r-consensusclusterplus
5842 (name "r-consensusclusterplus")
5847 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5850 "06gq3a95h0km1hzbx1za8q0l7kla3jdzvn6cnfz43ijx4n3dzzcq"))))
5852 `((upstream-name . "ConsensusClusterPlus")))
5853 (build-system r-build-system)
5856 ("r-biobase" ,r-biobase)
5857 ("r-cluster" ,r-cluster)))
5858 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5859 (synopsis "Clustering algorithm")
5861 "This package provides an implementation of an algorithm for determining
5862 cluster count and membership by stability evidence in unsupervised analysis.")
5863 (license license:gpl2)))
5865 (define-public r-cytolib
5872 (uri (bioconductor-uri "cytolib" version))
5875 "123d1wlymq8r8d83as380h1dgw6v4s317acyvp1lsg2cpfp3gslj"))))
5876 (properties `((upstream-name . "cytolib")))
5877 (build-system r-build-system)
5881 `(("r-knitr" ,r-knitr)))
5885 ("r-rcpparmadillo" ,r-rcpparmadillo)
5886 ("r-rcppparallel" ,r-rcppparallel)
5887 ("r-rhdf5lib" ,r-rhdf5lib)
5888 ("r-rprotobuflib" ,r-rprotobuflib)))
5889 (home-page "https://bioconductor.org/packages/cytolib/")
5890 (synopsis "C++ infrastructure for working with gated cytometry")
5892 "This package provides the core data structure and API to represent and
5893 interact with gated cytometry data.")
5894 (license license:artistic2.0)))
5896 (define-public r-flowcore
5903 (uri (bioconductor-uri "flowCore" version))
5906 "1xalndmfidfzqwlppdanx7cnm4ysznq21ingmykhxni86s42kd8p"))))
5907 (properties `((upstream-name . "flowCore")))
5908 (build-system r-build-system)
5911 ("r-biobase" ,r-biobase)
5912 ("r-biocgenerics" ,r-biocgenerics)
5913 ("r-cytolib" ,r-cytolib)
5914 ("r-matrixstats" ,r-matrixstats)
5916 ("r-rcpparmadillo" ,r-rcpparmadillo)
5917 ("r-rprotobuflib" ,r-rprotobuflib)))
5919 `(("r-knitr" ,r-knitr)))
5920 (home-page "https://bioconductor.org/packages/flowCore")
5921 (synopsis "Basic structures for flow cytometry data")
5923 "This package provides S4 data structures and basic functions to deal
5924 with flow cytometry data.")
5925 (license license:artistic2.0)))
5927 (define-public r-flowmeans
5929 (name "r-flowmeans")
5934 (uri (bioconductor-uri "flowMeans" version))
5937 "1sv5vpwm3qdhkn1gdrk3n674harjcni91g63sqzfmybiwq8dlym7"))))
5938 (properties `((upstream-name . "flowMeans")))
5939 (build-system r-build-system)
5941 `(("r-biobase" ,r-biobase)
5942 ("r-feature" ,r-feature)
5943 ("r-flowcore" ,r-flowcore)
5944 ("r-rrcov" ,r-rrcov)))
5945 (home-page "https://bioconductor.org/packages/flowMeans")
5946 (synopsis "Non-parametric flow cytometry data gating")
5948 "This package provides tools to identify cell populations in Flow
5949 Cytometry data using non-parametric clustering and segmented-regression-based
5950 change point detection.")
5951 (license license:artistic2.0)))
5953 (define-public r-ncdfflow
5960 (uri (bioconductor-uri "ncdfFlow" version))
5963 "0avxn2abh4fk1gkncrxz7jwzgvd90m3m0ly318q0z38cjhsw3j9f"))))
5964 (properties `((upstream-name . "ncdfFlow")))
5965 (build-system r-build-system)
5970 ("r-biobase" ,r-biobase)
5971 ("r-biocgenerics" ,r-biocgenerics)
5972 ("r-flowcore" ,r-flowcore)
5974 ("r-rcpparmadillo" ,r-rcpparmadillo)
5975 ("r-rhdf5lib" ,r-rhdf5lib)
5976 ("r-zlibbioc" ,r-zlibbioc)))
5978 `(("r-knitr" ,r-knitr)))
5979 (home-page "https://bioconductor.org/packages/ncdfFlow/")
5980 (synopsis "HDF5 based storage for flow cytometry data")
5982 "This package provides HDF5 storage based methods and functions for
5983 manipulation of flow cytometry data.")
5984 (license license:artistic2.0)))
5986 (define-public r-ggcyto
5993 (uri (bioconductor-uri "ggcyto" version))
5996 "1ih6ggay7jjxnx8blc2sk95g8d40gkim145jllkk8sqwl02g44p0"))))
5997 (properties `((upstream-name . "ggcyto")))
5998 (build-system r-build-system)
6000 `(("r-data-table" ,r-data-table)
6001 ("r-flowcore" ,r-flowcore)
6002 ("r-flowworkspace" ,r-flowworkspace)
6003 ("r-ggplot2" ,r-ggplot2)
6004 ("r-gridextra" ,r-gridextra)
6005 ("r-hexbin" ,r-hexbin)
6006 ("r-ncdfflow" ,r-ncdfflow)
6008 ("r-rcolorbrewer" ,r-rcolorbrewer)
6009 ("r-rlang" ,r-rlang)
6010 ("r-scales" ,r-scales)))
6012 `(("r-knitr" ,r-knitr)))
6013 (home-page "https://github.com/RGLab/ggcyto/issues")
6014 (synopsis "Visualize Cytometry data with ggplot")
6016 "With the dedicated fortify method implemented for @code{flowSet},
6017 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
6018 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
6019 and some custom layers also make it easy to add gates and population
6020 statistics to the plot.")
6021 (license license:artistic2.0)))
6023 (define-public r-flowviz
6030 (uri (bioconductor-uri "flowViz" version))
6033 "0f3jfwdmaq9wrgl737blk5gmpc29l9kb6nadqhxpvbjwqsnzx0yq"))))
6034 (properties `((upstream-name . "flowViz")))
6035 (build-system r-build-system)
6037 `(("r-biobase" ,r-biobase)
6038 ("r-flowcore" ,r-flowcore)
6039 ("r-hexbin" ,r-hexbin)
6040 ("r-idpmisc" ,r-idpmisc)
6041 ("r-kernsmooth" ,r-kernsmooth)
6042 ("r-lattice" ,r-lattice)
6043 ("r-latticeextra" ,r-latticeextra)
6045 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6047 `(("r-knitr" ,r-knitr)))
6048 (home-page "https://bioconductor.org/packages/flowViz/")
6049 (synopsis "Visualization for flow cytometry")
6051 "This package provides visualization tools for flow cytometry data.")
6052 (license license:artistic2.0)))
6054 (define-public r-flowclust
6056 (name "r-flowclust")
6061 (uri (bioconductor-uri "flowClust" version))
6064 "06mkq9y41jax07x4knhvhzgrkgqdvpvcw604bxdk6bv9wx3ipq5b"))))
6065 (properties `((upstream-name . "flowClust")))
6066 (build-system r-build-system)
6069 (list "--configure-args=--enable-bundled-gsl=no")))
6071 `(("r-biobase" ,r-biobase)
6072 ("r-biocgenerics" ,r-biocgenerics)
6074 ("r-corpcor" ,r-corpcor)
6075 ("r-ellipse" ,r-ellipse)
6076 ("r-flowcore" ,r-flowcore)
6077 ("r-flowviz" ,r-flowviz)
6078 ("r-graph" ,r-graph)
6079 ("r-mnormt" ,r-mnormt)))
6083 `(("pkg-config" ,pkg-config)
6084 ("r-knitr" ,r-knitr)))
6085 (home-page "https://bioconductor.org/packages/flowClust")
6086 (synopsis "Clustering for flow cytometry")
6088 "This package provides robust model-based clustering using a t-mixture
6089 model with Box-Cox transformation.")
6090 (license license:artistic2.0)))
6092 ;; TODO: this package bundles an old version of protobuf. It's not easy to
6093 ;; make it use our protobuf package instead.
6094 (define-public r-rprotobuflib
6096 (name "r-rprotobuflib")
6101 (uri (bioconductor-uri "RProtoBufLib" version))
6104 "0kfinf9vzc1i5qxmaw832id557gr1vqdi1m8yiaxz83g37wh8vps"))))
6105 (properties `((upstream-name . "RProtoBufLib")))
6106 (build-system r-build-system)
6109 (modify-phases %standard-phases
6110 (add-after 'unpack 'unpack-bundled-sources
6112 (with-directory-excursion "src"
6113 (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
6116 `(("r-knitr" ,r-knitr)))
6117 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
6118 (synopsis "C++ headers and static libraries of Protocol buffers")
6120 "This package provides the headers and static library of Protocol buffers
6121 for other R packages to compile and link against.")
6122 (license license:bsd-3)))
6124 (define-public r-flowworkspace
6126 (name "r-flowworkspace")
6131 (uri (bioconductor-uri "flowWorkspace" version))
6134 "123ny8n3jjgmsnpghk1dafxkwmcyr513gxi8y4h4qszq4s6ai15v"))))
6135 (properties `((upstream-name . "flowWorkspace")))
6136 (build-system r-build-system)
6139 ("r-biobase" ,r-biobase)
6140 ("r-biocgenerics" ,r-biocgenerics)
6141 ("r-cytolib" ,r-cytolib)
6142 ("r-data-table" ,r-data-table)
6143 ("r-digest" ,r-digest)
6144 ("r-dplyr" ,r-dplyr)
6145 ("r-flowcore" ,r-flowcore)
6146 ("r-ggplot2" ,r-ggplot2)
6147 ("r-graph" ,r-graph)
6148 ("r-lattice" ,r-lattice)
6149 ("r-latticeextra" ,r-latticeextra)
6150 ("r-matrixstats" ,r-matrixstats)
6151 ("r-ncdfflow" ,r-ncdfflow)
6154 ("r-rcpparmadillo" ,r-rcpparmadillo)
6155 ("r-rcppparallel" ,r-rcppparallel)
6156 ("r-rgraphviz" ,r-rgraphviz)
6157 ("r-rhdf5lib" ,r-rhdf5lib)
6158 ("r-rprotobuflib" ,r-rprotobuflib)
6159 ("r-scales" ,r-scales)
6160 ("r-stringr" ,r-stringr)
6163 `(("r-knitr" ,r-knitr)))
6164 (home-page "https://bioconductor.org/packages/flowWorkspace/")
6165 (synopsis "Infrastructure for working with cytometry data")
6167 "This package is designed to facilitate comparison of automated gating
6168 methods against manual gating done in flowJo. This package allows you to
6169 import basic flowJo workspaces into BioConductor and replicate the gating from
6170 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
6171 samples, compensation, and transformation are performed so that the output
6172 matches the flowJo analysis.")
6173 (license license:artistic2.0)))
6175 (define-public r-flowstats
6177 (name "r-flowstats")
6182 (uri (bioconductor-uri "flowStats" version))
6185 "1ygvxvd7y6jp907y0h3hycdwvw1fch16w84g06nk4f4g4kvrzdir"))))
6186 (properties `((upstream-name . "flowStats")))
6187 (build-system r-build-system)
6189 `(("r-biobase" ,r-biobase)
6190 ("r-biocgenerics" ,r-biocgenerics)
6191 ("r-cluster" ,r-cluster)
6193 ("r-flowcore" ,r-flowcore)
6194 ("r-flowviz" ,r-flowviz)
6195 ("r-flowworkspace" ,r-flowworkspace)
6196 ("r-kernsmooth" ,r-kernsmooth)
6198 ("r-lattice" ,r-lattice)
6200 ("r-ncdfflow" ,r-ncdfflow)
6201 ("r-rcolorbrewer" ,r-rcolorbrewer)
6202 ("r-rrcov" ,r-rrcov)))
6203 (home-page "http://www.github.com/RGLab/flowStats")
6204 (synopsis "Statistical methods for the analysis of flow cytometry data")
6206 "This package provides methods and functionality to analyze flow data
6207 that is beyond the basic infrastructure provided by the @code{flowCore}
6209 (license license:artistic2.0)))
6211 (define-public r-opencyto
6218 (uri (bioconductor-uri "openCyto" version))
6221 "10dyd6dddskv70vhpwfbsqdb8pb9i3ka0fgvl1h51wqlckbsj89m"))))
6222 (properties `((upstream-name . "openCyto")))
6223 (build-system r-build-system)
6225 `(("r-biobase" ,r-biobase)
6226 ("r-biocgenerics" ,r-biocgenerics)
6228 ("r-data-table" ,r-data-table)
6229 ("r-flowclust" ,r-flowclust)
6230 ("r-flowcore" ,r-flowcore)
6231 ("r-flowstats" ,r-flowstats)
6232 ("r-flowviz" ,r-flowviz)
6233 ("r-flowworkspace" ,r-flowworkspace)
6234 ("r-graph" ,r-graph)
6235 ("r-gtools" ,r-gtools)
6237 ("r-lattice" ,r-lattice)
6239 ("r-ncdfflow" ,r-ncdfflow)
6241 ("r-r-utils" ,r-r-utils)
6243 ("r-rcolorbrewer" ,r-rcolorbrewer)
6245 ("r-rrcov" ,r-rrcov)))
6247 `(("r-knitr" ,r-knitr)))
6248 (home-page "https://bioconductor.org/packages/openCyto")
6249 (synopsis "Hierarchical gating pipeline for flow cytometry data")
6251 "This package is designed to facilitate the automated gating methods in a
6252 sequential way to mimic the manual gating strategy.")
6253 (license license:artistic2.0)))
6255 (define-public r-cytoml
6262 (uri (bioconductor-uri "CytoML" version))
6265 "174brv027mm90lydfg6hnhazwh8jy4vf6ial4hpsfalwa5jrz55n"))))
6266 (properties `((upstream-name . "CytoML")))
6267 (build-system r-build-system)
6269 `(("libxml2" ,libxml2)))
6271 `(("r-base64enc" ,r-base64enc)
6273 ("r-biobase" ,r-biobase)
6274 ("r-corpcor" ,r-corpcor)
6275 ("r-cytolib" ,r-cytolib)
6276 ("r-data-table" ,r-data-table)
6277 ("r-dplyr" ,r-dplyr)
6278 ("r-flowcore" ,r-flowcore)
6279 ("r-flowworkspace" ,r-flowworkspace)
6280 ("r-ggcyto" ,r-ggcyto)
6281 ("r-graph" ,r-graph)
6282 ("r-jsonlite" ,r-jsonlite)
6283 ("r-lattice" ,r-lattice)
6284 ("r-opencyto" ,r-opencyto)
6288 ("r-rcpparmadillo" ,r-rcpparmadillo)
6289 ("r-rcppparallel" ,r-rcppparallel)
6290 ("r-rgraphviz" ,r-rgraphviz)
6291 ("r-rhdf5lib" ,r-rhdf5lib)
6292 ("r-rprotobuflib" ,r-rprotobuflib)
6293 ("r-runit" ,r-runit)
6294 ("r-tibble" ,r-tibble)
6297 ("r-yaml" ,r-yaml)))
6299 `(("r-knitr" ,r-knitr)))
6300 (home-page "https://github.com/RGLab/CytoML")
6301 (synopsis "GatingML interface for cross platform cytometry data sharing")
6303 "This package provides an interface to implementations of the GatingML2.0
6304 standard to exchange gated cytometry data with other software platforms.")
6305 (license license:artistic2.0)))
6307 (define-public r-flowsom
6314 (uri (bioconductor-uri "FlowSOM" version))
6317 "1p17jv4q1dbcc47jpjy9hbcvzpwrx8waq7qpcj778jsyz6z6jh78"))))
6318 (properties `((upstream-name . "FlowSOM")))
6319 (build-system r-build-system)
6321 `(("r-biocgenerics" ,r-biocgenerics)
6322 ("r-consensusclusterplus" ,r-consensusclusterplus)
6323 ("r-cytoml" ,r-cytoml)
6324 ("r-flowcore" ,r-flowcore)
6325 ("r-flowworkspace" ,r-flowworkspace)
6326 ("r-igraph" ,r-igraph)
6327 ("r-rcolorbrewer" ,r-rcolorbrewer)
6330 (home-page "https://bioconductor.org/packages/FlowSOM/")
6331 (synopsis "Visualize and interpret cytometry data")
6333 "FlowSOM offers visualization options for cytometry data, by using
6334 self-organizing map clustering and minimal spanning trees.")
6335 (license license:gpl2+)))
6337 (define-public r-mixomics
6344 (uri (bioconductor-uri "mixOmics" version))
6347 "1nkqlvm9j1f4vfj3f3kyxqgan38rpa9imimvl9pwivvsfl647vvc"))))
6348 (properties `((upstream-name . "mixOmics")))
6349 (build-system r-build-system)
6351 `(("r-corpcor" ,r-corpcor)
6352 ("r-dplyr" ,r-dplyr)
6353 ("r-ellipse" ,r-ellipse)
6354 ("r-ggplot2" ,r-ggplot2)
6355 ("r-gridextra" ,r-gridextra)
6356 ("r-igraph" ,r-igraph)
6357 ("r-lattice" ,r-lattice)
6359 ("r-matrixstats" ,r-matrixstats)
6360 ("r-rarpack" ,r-rarpack)
6361 ("r-rcolorbrewer" ,r-rcolorbrewer)
6362 ("r-reshape2" ,r-reshape2)
6363 ("r-tidyr" ,r-tidyr)))
6365 `(("r-knitr" ,r-knitr)))
6366 (home-page "http://www.mixOmics.org")
6367 (synopsis "Multivariate methods for exploration of biological datasets")
6369 "mixOmics offers a wide range of multivariate methods for the exploration
6370 and integration of biological datasets with a particular focus on variable
6371 selection. The package proposes several sparse multivariate models we have
6372 developed to identify the key variables that are highly correlated, and/or
6373 explain the biological outcome of interest. The data that can be analysed
6374 with mixOmics may come from high throughput sequencing technologies, such as
6375 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
6376 also beyond the realm of omics (e.g. spectral imaging). The methods
6377 implemented in mixOmics can also handle missing values without having to
6378 delete entire rows with missing data.")
6379 (license license:gpl2+)))
6381 (define-public r-depecher
6388 (uri (bioconductor-uri "DepecheR" version))
6391 "0dscfl6wxpl5538jzkrwisdwbr873d38rzd19vl6z5br71jvpv3v"))))
6392 (properties `((upstream-name . "DepecheR")))
6393 (build-system r-build-system)
6395 `(("r-beanplot" ,r-beanplot)
6396 ("r-dosnow" ,r-dosnow)
6397 ("r-dplyr" ,r-dplyr)
6399 ("r-foreach" ,r-foreach)
6400 ("r-ggplot2" ,r-ggplot2)
6401 ("r-gplots" ,r-gplots)
6403 ("r-matrixstats" ,r-matrixstats)
6404 ("r-mixomics" ,r-mixomics)
6405 ("r-moments" ,r-moments)
6407 ("r-rcppeigen" ,r-rcppeigen)
6408 ("r-reshape2" ,r-reshape2)
6409 ("r-robustbase" ,r-robustbase)
6410 ("r-viridis" ,r-viridis)))
6412 `(("r-knitr" ,r-knitr)))
6413 (home-page "https://bioconductor.org/packages/DepecheR/")
6414 (synopsis "Identify traits of clusters in high-dimensional entities")
6416 "The purpose of this package is to identify traits in a dataset that can
6417 separate groups. This is done on two levels. First, clustering is performed,
6418 using an implementation of sparse K-means. Secondly, the generated clusters
6419 are used to predict outcomes of groups of individuals based on their
6420 distribution of observations in the different clusters. As certain clusters
6421 with separating information will be identified, and these clusters are defined
6422 by a sparse number of variables, this method can reduce the complexity of
6423 data, to only emphasize the data that actually matters.")
6424 (license license:expat)))
6426 (define-public r-rcistarget
6428 (name "r-rcistarget")
6433 (uri (bioconductor-uri "RcisTarget" version))
6436 "1lvi873dv0vhw53s1pmcilw8qwlywm9p2ybphcl168nzh6w31r4i"))))
6437 (properties `((upstream-name . "RcisTarget")))
6438 (build-system r-build-system)
6440 `(("r-aucell" ,r-aucell)
6441 ("r-biocgenerics" ,r-biocgenerics)
6442 ("r-data-table" ,r-data-table)
6443 ("r-feather" ,r-feather)
6444 ("r-gseabase" ,r-gseabase)
6445 ("r-r-utils" ,r-r-utils)
6446 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6448 `(("r-knitr" ,r-knitr)))
6449 (home-page "https://aertslab.org/#scenic")
6450 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
6452 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
6453 over-represented on a gene list. In a first step, RcisTarget selects DNA
6454 motifs that are significantly over-represented in the surroundings of the
6455 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
6456 achieved by using a database that contains genome-wide cross-species rankings
6457 for each motif. The motifs that are then annotated to TFs and those that have
6458 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
6459 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
6460 genes in the gene-set that are ranked above the leading edge).")
6461 (license license:gpl3)))
6463 (define-public r-cicero
6470 (uri (bioconductor-uri "cicero" version))
6473 "042ba6yfa7fksij2v7cwnp2sca3vmz7izn6fsxx9xswnncrkgcqh"))))
6474 (build-system r-build-system)
6476 `(("r-assertthat" ,r-assertthat)
6477 ("r-biobase" ,r-biobase)
6478 ("r-biocgenerics" ,r-biocgenerics)
6479 ("r-data-table" ,r-data-table)
6480 ("r-dplyr" ,r-dplyr)
6482 ("r-genomicranges" ,r-genomicranges)
6483 ("r-ggplot2" ,r-ggplot2)
6484 ("r-glasso" ,r-glasso)
6486 ("r-igraph" ,r-igraph)
6487 ("r-iranges" ,r-iranges)
6488 ("r-matrix" ,r-matrix)
6489 ("r-monocle" ,r-monocle)
6491 ("r-reshape2" ,r-reshape2)
6492 ("r-s4vectors" ,r-s4vectors)
6493 ("r-stringi" ,r-stringi)
6494 ("r-stringr" ,r-stringr)
6495 ("r-tibble" ,r-tibble)
6496 ("r-tidyr" ,r-tidyr)
6497 ("r-vgam" ,r-vgam)))
6499 `(("r-knitr" ,r-knitr)))
6500 (home-page "https://bioconductor.org/packages/cicero/")
6501 (synopsis "Predict cis-co-accessibility from single-cell data")
6503 "Cicero computes putative cis-regulatory maps from single-cell chromatin
6504 accessibility data. It also extends the monocle package for use in chromatin
6505 accessibility data.")
6506 (license license:expat)))
6508 ;; This is the latest commit on the "monocle3" branch.
6509 (define-public r-cicero-monocle3
6510 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
6512 (package (inherit r-cicero)
6513 (name "r-cicero-monocle3")
6514 (version (git-version "1.3.2" revision commit))
6519 (url "https://github.com/cole-trapnell-lab/cicero-release")
6521 (file-name (git-file-name name version))
6524 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
6526 `(("r-monocle3" ,r-monocle3)
6527 ,@(alist-delete "r-monocle"
6528 (package-propagated-inputs r-cicero)))))))
6530 (define-public r-cistopic
6531 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
6535 (version (git-version "0.2.1" revision commit))
6540 (url "https://github.com/aertslab/cisTopic")
6542 (file-name (git-file-name name version))
6545 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
6546 (build-system r-build-system)
6548 `(("r-aucell" ,r-aucell)
6549 ("r-data-table" ,r-data-table)
6550 ("r-dplyr" ,r-dplyr)
6551 ("r-dosnow" ,r-dosnow)
6553 ("r-feather" ,r-feather)
6554 ("r-fitdistrplus" ,r-fitdistrplus)
6555 ("r-genomicranges" ,r-genomicranges)
6556 ("r-ggplot2" ,r-ggplot2)
6558 ("r-matrix" ,r-matrix)
6560 ("r-rcistarget" ,r-rcistarget)
6561 ("r-rtracklayer" ,r-rtracklayer)
6562 ("r-s4vectors" ,r-s4vectors)))
6563 (home-page "https://github.com/aertslab/cisTopic")
6564 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
6566 "The sparse nature of single cell epigenomics data can be overruled using
6567 probabilistic modelling methods such as @dfn{Latent Dirichlet
6568 Allocation} (LDA). This package allows the probabilistic modelling of
6569 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
6570 includes functionalities to identify cell states based on the contribution of
6571 cisTopics and explore the nature and regulatory proteins driving them.")
6572 (license license:gpl3))))
6574 (define-public r-genie3
6581 (uri (bioconductor-uri "GENIE3" version))
6584 "1bsm0gxracsyg1wnaw3whvskghfpbgbm9navr8wdmxj2hjp3dqs7"))))
6585 (properties `((upstream-name . "GENIE3")))
6586 (build-system r-build-system)
6587 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
6589 `(("r-knitr" ,r-knitr)))
6590 (home-page "https://bioconductor.org/packages/GENIE3")
6591 (synopsis "Gene network inference with ensemble of trees")
6593 "This package implements the GENIE3 algorithm for inferring gene
6594 regulatory networks from expression data.")
6595 (license license:gpl2+)))
6597 (define-public r-roc
6604 (uri (bioconductor-uri "ROC" version))
6607 "0gmx3r77yl5fqrj5j2hamwynbis75qd62q28964kx16z33xfgx89"))))
6608 (properties `((upstream-name . "ROC")))
6609 (build-system r-build-system)
6611 `(("r-knitr" ,r-knitr)))
6612 (home-page "https://www.bioconductor.org/packages/ROC/")
6613 (synopsis "Utilities for ROC curves")
6615 "This package provides utilities for @dfn{Receiver Operating
6616 Characteristic} (ROC) curves, with a focus on micro arrays.")
6617 (license license:artistic2.0)))
6619 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
6621 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
6626 (uri (bioconductor-uri
6627 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
6628 version 'annotation))
6631 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
6634 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
6635 (build-system r-build-system)
6636 (propagated-inputs `(("r-minfi" ,r-minfi)))
6638 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
6639 (synopsis "Annotation for Illumina's 450k methylation arrays")
6641 "This package provides manifests and annotation for Illumina's 450k array
6643 (license license:artistic2.0)))
6645 (define-public r-watermelon
6647 (name "r-watermelon")
6652 (uri (bioconductor-uri "wateRmelon" version))
6655 "1c3a6bq3ggmv8kmdfrgiar6nwgircgzjrbgd9z9dqiin7j13gxwn"))))
6656 (properties `((upstream-name . "wateRmelon")))
6657 (build-system r-build-system)
6659 `(("r-biobase" ,r-biobase)
6660 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
6661 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
6662 ("r-illuminaio" ,r-illuminaio)
6663 ("r-limma" ,r-limma)
6665 ("r-matrixstats" ,r-matrixstats)
6666 ("r-methylumi" ,r-methylumi)
6668 (home-page "https://bioconductor.org/packages/wateRmelon/")
6669 (synopsis "Illumina 450 methylation array normalization and metrics")
6671 "The standard index of DNA methylation (beta) is computed from methylated
6672 and unmethylated signal intensities. Betas calculated from raw signal
6673 intensities perform well, but using 11 methylomic datasets we demonstrate that
6674 quantile normalization methods produce marked improvement. The commonly used
6675 procedure of normalizing betas is inferior to the separate normalization of M
6676 and U, and it is also advantageous to normalize Type I and Type II assays
6677 separately. This package provides 15 flavours of betas and three performance
6678 metrics, with methods for objects produced by the @code{methylumi} and
6679 @code{minfi} packages.")
6680 (license license:gpl3)))
6682 (define-public r-gdsfmt
6689 (uri (bioconductor-uri "gdsfmt" version))
6692 "0ipf60wylbhvwk9q3mbnak0f1n6k7spfh90s1c1c0b47ryxsri67"))
6693 (modules '((guix build utils)))
6694 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
6695 ;; them and link with system libraries instead.
6698 (for-each delete-file-recursively
6702 (substitute* "src/Makevars"
6703 (("all: \\$\\(SHLIB\\)") "all:")
6704 (("\\$\\(SHLIB\\): liblzma.a") "")
6705 (("(ZLIB|LZ4)/.*") "")
6706 (("CoreArray/dVLIntGDS.cpp.*")
6707 "CoreArray/dVLIntGDS.cpp")
6708 (("CoreArray/dVLIntGDS.o.*")
6709 "CoreArray/dVLIntGDS.o")
6710 (("PKG_LIBS = ./liblzma.a")
6711 "PKG_LIBS = -llz4"))
6712 (substitute* "src/CoreArray/dStream.h"
6713 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
6714 (string-append "include <" header ">")))
6716 (properties `((upstream-name . "gdsfmt")))
6717 (build-system r-build-system)
6723 `(("r-knitr" ,r-knitr)))
6724 (home-page "http://corearray.sourceforge.net/")
6726 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
6728 "This package provides a high-level R interface to CoreArray @dfn{Genomic
6729 Data Structure} (GDS) data files, which are portable across platforms with
6730 hierarchical structure to store multiple scalable array-oriented data sets
6731 with metadata information. It is suited for large-scale datasets, especially
6732 for data which are much larger than the available random-access memory. The
6733 @code{gdsfmt} package offers efficient operations specifically designed for
6734 integers of less than 8 bits, since a diploid genotype, like
6735 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
6736 byte. Data compression and decompression are available with relatively
6737 efficient random access. It is also allowed to read a GDS file in parallel
6738 with multiple R processes supported by the package @code{parallel}.")
6739 (license license:lgpl3)))
6741 (define-public r-bigmelon
6748 (uri (bioconductor-uri "bigmelon" version))
6751 "1cryjhbiacm45g097rpqgbva49hs5vdx4y4h5h2v1gw4k78hwb4y"))))
6752 (properties `((upstream-name . "bigmelon")))
6753 (build-system r-build-system)
6755 `(("r-biobase" ,r-biobase)
6756 ("r-biocgenerics" ,r-biocgenerics)
6757 ("r-gdsfmt" ,r-gdsfmt)
6758 ("r-geoquery" ,r-geoquery)
6759 ("r-methylumi" ,r-methylumi)
6760 ("r-minfi" ,r-minfi)
6761 ("r-watermelon" ,r-watermelon)))
6762 (home-page "https://bioconductor.org/packages/bigmelon/")
6763 (synopsis "Illumina methylation array analysis for large experiments")
6765 "This package provides methods for working with Illumina arrays using the
6766 @code{gdsfmt} package.")
6767 (license license:gpl3)))
6769 (define-public r-seqbias
6776 (uri (bioconductor-uri "seqbias" version))
6779 "0sy2fv98x4qfz9llns28jh1n4bi991jj856y8a5fbzpx7y990lai"))))
6780 (properties `((upstream-name . "seqbias")))
6781 (build-system r-build-system)
6783 `(("r-biostrings" ,r-biostrings)
6784 ("r-genomicranges" ,r-genomicranges)
6785 ("r-rhtslib" ,r-rhtslib)))
6787 `(("zlib" ,zlib))) ; This comes from rhtslib.
6788 (home-page "https://bioconductor.org/packages/seqbias/")
6789 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
6791 "This package implements a model of per-position sequencing bias in
6792 high-throughput sequencing data using a simple Bayesian network, the structure
6793 and parameters of which are trained on a set of aligned reads and a reference
6795 (license license:lgpl3)))
6797 (define-public r-snplocs-hsapiens-dbsnp144-grch37
6799 (name "r-snplocs-hsapiens-dbsnp144-grch37")
6803 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
6804 version 'annotation))
6807 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
6808 (build-system r-build-system)
6809 ;; As this package provides little more than a very large data file it
6810 ;; doesn't make sense to build substitutes.
6811 (arguments `(#:substitutable? #f))
6813 `(("r-biocgenerics" ,r-biocgenerics)
6814 ("r-s4vectors" ,r-s4vectors)
6815 ("r-iranges" ,r-iranges)
6816 ("r-genomeinfodb" ,r-genomeinfodb)
6817 ("r-genomicranges" ,r-genomicranges)
6818 ("r-bsgenome" ,r-bsgenome)
6819 ("r-biostrings" ,r-biostrings)))
6821 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
6822 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
6823 (description "This package provides SNP locations and alleles for Homo
6824 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
6825 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
6826 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
6827 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
6828 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
6829 the mitochondrion chromosome. Therefore, the SNPs in this package can be
6830 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
6831 correct position but this injection will exclude chrM (i.e. nothing will be
6832 injected in that sequence).")
6833 (license license:artistic2.0)))
6835 (define-public r-reqon
6842 (uri (bioconductor-uri "ReQON" version))
6845 "06m0hd4aqsxjyzhs8b1zys7lz8289qgwn7jp2dpln1j7cf02q4bz"))))
6846 (properties `((upstream-name . "ReQON")))
6847 (build-system r-build-system)
6849 `(("r-rjava" ,r-rjava)
6850 ("r-rsamtools" ,r-rsamtools)
6851 ("r-seqbias" ,r-seqbias)))
6852 (home-page "https://bioconductor.org/packages/ReQON/")
6853 (synopsis "Recalibrating quality of nucleotides")
6855 "This package provides an implementation of an algorithm for
6856 recalibrating the base quality scores for aligned sequencing data in BAM
6858 (license license:gpl2)))
6860 (define-public r-wavcluster
6862 (name "r-wavcluster")
6867 (uri (bioconductor-uri "wavClusteR" version))
6870 "0204czqjmkwhd6gznwxzb0vj3dg3aif628g8c30085aa2jljn9bk"))))
6871 (properties `((upstream-name . "wavClusteR")))
6872 (build-system r-build-system)
6874 `(("r-biocgenerics" ,r-biocgenerics)
6875 ("r-biostrings" ,r-biostrings)
6876 ("r-foreach" ,r-foreach)
6877 ("r-genomicfeatures" ,r-genomicfeatures)
6878 ("r-genomicranges" ,r-genomicranges)
6879 ("r-ggplot2" ,r-ggplot2)
6880 ("r-hmisc" ,r-hmisc)
6881 ("r-iranges" ,r-iranges)
6882 ("r-mclust" ,r-mclust)
6883 ("r-rsamtools" ,r-rsamtools)
6884 ("r-rtracklayer" ,r-rtracklayer)
6885 ("r-s4vectors" ,r-s4vectors)
6886 ("r-seqinr" ,r-seqinr)
6887 ("r-stringr" ,r-stringr)
6888 ("r-wmtsa" ,r-wmtsa)))
6890 `(("r-knitr" ,r-knitr)))
6891 (home-page "https://bioconductor.org/packages/wavClusteR/")
6892 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
6894 "This package provides an integrated pipeline for the analysis of
6895 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
6896 sequencing errors, SNPs and additional non-experimental sources by a non-
6897 parametric mixture model. The protein binding sites (clusters) are then
6898 resolved at high resolution and cluster statistics are estimated using a
6899 rigorous Bayesian framework. Post-processing of the results, data export for
6900 UCSC genome browser visualization and motif search analysis are provided. In
6901 addition, the package integrates RNA-Seq data to estimate the False
6902 Discovery Rate of cluster detection. Key functions support parallel multicore
6903 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
6904 be applied to the analysis of other NGS data obtained from experimental
6905 procedures that induce nucleotide substitutions (e.g. BisSeq).")
6906 (license license:gpl2)))
6908 (define-public r-timeseriesexperiment
6910 (name "r-timeseriesexperiment")
6915 (uri (bioconductor-uri "TimeSeriesExperiment" version))
6918 "1k0djvcsyjj1ayncvmi8nlqi3jdn5qp41y3fwsqg1cp0qsvx7zv3"))))
6920 `((upstream-name . "TimeSeriesExperiment")))
6921 (build-system r-build-system)
6923 `(("r-deseq2" ,r-deseq2)
6924 ("r-dplyr" ,r-dplyr)
6925 ("r-dynamictreecut" ,r-dynamictreecut)
6926 ("r-edger" ,r-edger)
6927 ("r-ggplot2" ,r-ggplot2)
6928 ("r-hmisc" ,r-hmisc)
6929 ("r-limma" ,r-limma)
6930 ("r-magrittr" ,r-magrittr)
6931 ("r-proxy" ,r-proxy)
6932 ("r-s4vectors" ,r-s4vectors)
6933 ("r-summarizedexperiment" ,r-summarizedexperiment)
6934 ("r-tibble" ,r-tibble)
6935 ("r-tidyr" ,r-tidyr)
6936 ("r-vegan" ,r-vegan)
6937 ("r-viridis" ,r-viridis)))
6939 `(("r-knitr" ,r-knitr)))
6940 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
6941 (synopsis "Analysis for short time-series data")
6943 "This package is a visualization and analysis toolbox for short time
6944 course data which includes dimensionality reduction, clustering, two-sample
6945 differential expression testing and gene ranking techniques. The package also
6946 provides methods for retrieving enriched pathways.")
6947 (license license:lgpl3+)))
6949 (define-public r-variantfiltering
6951 (name "r-variantfiltering")
6956 (uri (bioconductor-uri "VariantFiltering" version))
6959 "0lsrnybsbm9siyjv4nal6bmprj8ynwgk4n1145f4h52g78wq3br4"))))
6961 `((upstream-name . "VariantFiltering")))
6962 (build-system r-build-system)
6964 `(("r-annotationdbi" ,r-annotationdbi)
6965 ("r-biobase" ,r-biobase)
6966 ("r-biocgenerics" ,r-biocgenerics)
6967 ("r-biocparallel" ,r-biocparallel)
6968 ("r-biostrings" ,r-biostrings)
6969 ("r-bsgenome" ,r-bsgenome)
6971 ("r-genomeinfodb" ,r-genomeinfodb)
6972 ("r-genomicfeatures" ,r-genomicfeatures)
6973 ("r-genomicranges" ,r-genomicranges)
6974 ("r-genomicscores" ,r-genomicscores)
6975 ("r-graph" ,r-graph)
6977 ("r-iranges" ,r-iranges)
6979 ("r-rsamtools" ,r-rsamtools)
6980 ("r-s4vectors" ,r-s4vectors)
6981 ("r-shiny" ,r-shiny)
6982 ("r-shinyjs" ,r-shinyjs)
6983 ("r-shinythemes" ,r-shinythemes)
6984 ("r-shinytree" ,r-shinytree)
6985 ("r-summarizedexperiment" ,r-summarizedexperiment)
6986 ("r-variantannotation" ,r-variantannotation)
6987 ("r-xvector" ,r-xvector)))
6988 (home-page "https://github.com/rcastelo/VariantFiltering")
6989 (synopsis "Filtering of coding and non-coding genetic variants")
6991 "Filter genetic variants using different criteria such as inheritance
6992 model, amino acid change consequence, minor allele frequencies across human
6993 populations, splice site strength, conservation, etc.")
6994 (license license:artistic2.0)))
6996 (define-public r-genomegraphs
6998 (name "r-genomegraphs")
7003 (uri (bioconductor-uri "GenomeGraphs" version))
7006 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
7007 (properties `((upstream-name . "GenomeGraphs")))
7008 (build-system r-build-system)
7010 `(("r-biomart" ,r-biomart)))
7011 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
7012 (synopsis "Plotting genomic information from Ensembl")
7014 "Genomic data analyses requires integrated visualization of known genomic
7015 information and new experimental data. GenomeGraphs uses the biomaRt package
7016 to perform live annotation queries to Ensembl and translates this to e.g.
7017 gene/transcript structures in viewports of the grid graphics package. This
7018 results in genomic information plotted together with your data. Another
7019 strength of GenomeGraphs is to plot different data types such as array CGH,
7020 gene expression, sequencing and other data, together in one plot using the
7021 same genome coordinate system.")
7022 (license license:artistic2.0)))
7024 (define-public r-wavetiling
7026 (name "r-wavetiling")
7031 (uri (bioconductor-uri "waveTiling" version))
7034 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
7035 (properties `((upstream-name . "waveTiling")))
7036 (build-system r-build-system)
7038 `(("r-affy" ,r-affy)
7039 ("r-biobase" ,r-biobase)
7040 ("r-biostrings" ,r-biostrings)
7041 ("r-genomegraphs" ,r-genomegraphs)
7042 ("r-genomicranges" ,r-genomicranges)
7043 ("r-iranges" ,r-iranges)
7044 ("r-oligo" ,r-oligo)
7045 ("r-oligoclasses" ,r-oligoclasses)
7046 ("r-preprocesscore" ,r-preprocesscore)
7047 ("r-waveslim" ,r-waveslim)))
7048 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
7049 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
7051 "This package is designed to conduct transcriptome analysis for tiling
7052 arrays based on fast wavelet-based functional models.")
7053 (license license:gpl2+)))
7055 (define-public r-variancepartition
7057 (name "r-variancepartition")
7062 (uri (bioconductor-uri "variancePartition" version))
7065 "1jrlhi2c5ibvq8a41g5hwdq4kk4rdd7m464rz5767zaaci7l2ay0"))))
7067 `((upstream-name . "variancePartition")))
7068 (build-system r-build-system)
7070 `(("r-biobase" ,r-biobase)
7071 ("r-biocparallel" ,r-biocparallel)
7072 ("r-colorramps" ,r-colorramps)
7073 ("r-doparallel" ,r-doparallel)
7074 ("r-foreach" ,r-foreach)
7075 ("r-ggplot2" ,r-ggplot2)
7076 ("r-gplots" ,r-gplots)
7077 ("r-iterators" ,r-iterators)
7078 ("r-limma" ,r-limma)
7080 ("r-lmertest" ,r-lmertest)
7082 ("r-pbkrtest" ,r-pbkrtest)
7083 ("r-progress" ,r-progress)
7084 ("r-reshape2" ,r-reshape2)
7085 ("r-scales" ,r-scales)))
7087 `(("r-knitr" ,r-knitr)))
7088 (home-page "https://bioconductor.org/packages/variancePartition/")
7089 (synopsis "Analyze variation in gene expression experiments")
7091 "This is a package providing tools to quantify and interpret multiple
7092 sources of biological and technical variation in gene expression experiments.
7093 It uses a linear mixed model to quantify variation in gene expression
7094 attributable to individual, tissue, time point, or technical variables. The
7095 package includes dream differential expression analysis for repeated
7097 (license license:gpl2+)))
7099 (define-public r-htqpcr
7106 (uri (bioconductor-uri "HTqPCR" version))
7109 "08bd5zkjdnz726s03bvvzv03va0xbrr818ipp6737z9g3nk9m81j"))))
7110 (properties `((upstream-name . "HTqPCR")))
7111 (build-system r-build-system)
7113 `(("r-affy" ,r-affy)
7114 ("r-biobase" ,r-biobase)
7115 ("r-gplots" ,r-gplots)
7116 ("r-limma" ,r-limma)
7117 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7118 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
7119 "groups/bertone/software/HTqPCR.pdf"))
7120 (synopsis "Automated analysis of high-throughput qPCR data")
7122 "Analysis of Ct values from high throughput quantitative real-time
7123 PCR (qPCR) assays across multiple conditions or replicates. The input data
7124 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
7125 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
7126 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
7127 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
7128 loading, quality assessment, normalization, visualization and parametric or
7129 non-parametric testing for statistical significance in Ct values between
7130 features (e.g. genes, microRNAs).")
7131 (license license:artistic2.0)))
7133 (define-public r-unifiedwmwqpcr
7135 (name "r-unifiedwmwqpcr")
7140 (uri (bioconductor-uri "unifiedWMWqPCR" version))
7143 "1l9gxq3askr3cz2a4bqsw7vjr1agivzvx651cblkygv57x08zf81"))))
7145 `((upstream-name . "unifiedWMWqPCR")))
7146 (build-system r-build-system)
7148 `(("r-biocgenerics" ,r-biocgenerics)
7149 ("r-htqpcr" ,r-htqpcr)))
7150 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
7151 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
7153 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
7154 data. This modified test allows for testing differential expression in qPCR
7156 (license license:gpl2+)))
7158 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7160 (define-public r-activedriverwgs
7162 (name "r-activedriverwgs")
7167 (uri (cran-uri "ActiveDriverWGS" version))
7170 "0l6h0f54zjvcx19ngq3kp01dypsjqf28vssjm8yzccmpyacfypag"))))
7172 `((upstream-name . "ActiveDriverWGS")))
7173 (build-system r-build-system)
7175 `(("r-biostrings" ,r-biostrings)
7176 ("r-bsgenome" ,r-bsgenome)
7177 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7178 ("r-genomeinfodb" ,r-genomeinfodb)
7179 ("r-genomicranges" ,r-genomicranges)
7180 ("r-iranges" ,r-iranges)
7181 ("r-s4vectors" ,r-s4vectors)))
7183 `(("r-knitr" ,r-knitr)))
7184 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
7185 (synopsis "Driver discovery tool for cancer whole genomes")
7187 "This package provides a method for finding an enrichment of cancer
7188 simple somatic mutations (SNVs and Indels) in functional elements across the
7189 human genome. ActiveDriverWGS detects coding and noncoding driver elements
7190 using whole genome sequencing data.")
7191 (license license:gpl3)))
7193 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7195 (define-public r-activepathways
7197 (name "r-activepathways")
7202 (uri (cran-uri "ActivePathways" version))
7205 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
7207 `((upstream-name . "ActivePathways")))
7208 (build-system r-build-system)
7210 `(("r-data-table" ,r-data-table)
7211 ("r-ggplot2" ,r-ggplot2)))
7213 `(("r-knitr" ,r-knitr)))
7214 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
7215 (synopsis "Multivariate pathway enrichment analysis")
7217 "This package represents an integrative method of analyzing multi omics
7218 data that conducts enrichment analysis of annotated gene sets. ActivePathways
7219 uses a statistical data fusion approach, rationalizes contributing evidence
7220 and highlights associated genes, improving systems-level understanding of
7221 cellular organization in health and disease.")
7222 (license license:gpl3)))
7224 (define-public r-bgmix
7231 (uri (bioconductor-uri "BGmix" version))
7234 "1pfi3hinjn6ymikadgj8dqm59h7mapf01wj86dbbvf8y1xqp8y8n"))))
7235 (properties `((upstream-name . "BGmix")))
7236 (build-system r-build-system)
7238 `(("r-kernsmooth" ,r-kernsmooth)))
7239 (home-page "https://bioconductor.org/packages/BGmix/")
7240 (synopsis "Bayesian models for differential gene expression")
7242 "This package provides fully Bayesian mixture models for differential
7244 (license license:gpl2)))
7246 (define-public r-bgx
7253 (uri (bioconductor-uri "bgx" version))
7256 "0r67a6m5hrnsxgk0f57hl5yaagi2wai2kpfyjjlhrck4rlm1sjcx"))))
7257 (properties `((upstream-name . "bgx")))
7258 (build-system r-build-system)
7260 `(("r-affy" ,r-affy)
7261 ("r-biobase" ,r-biobase)
7262 ("r-gcrma" ,r-gcrma)
7263 ("r-rcpp" ,r-rcpp)))
7264 (home-page "https://bioconductor.org/packages/bgx/")
7265 (synopsis "Bayesian gene expression")
7267 "This package provides tools for Bayesian integrated analysis of
7268 Affymetrix GeneChips.")
7269 (license license:gpl2)))
7271 (define-public r-bhc
7278 (uri (bioconductor-uri "BHC" version))
7281 "06milqjg2nl3ra47sxi7a2p2d3mbrx3wk168pqgimvs8snldd2xr"))))
7282 (properties `((upstream-name . "BHC")))
7283 (build-system r-build-system)
7284 (home-page "https://bioconductor.org/packages/BHC/")
7285 (synopsis "Bayesian hierarchical clustering")
7287 "The method implemented in this package performs bottom-up hierarchical
7288 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
7289 in the data and Bayesian model selection to decide at each step which clusters
7290 to merge. This avoids several limitations of traditional methods, for example
7291 how many clusters there should be and how to choose a principled distance
7292 metric. This implementation accepts multinomial (i.e. discrete, with 2+
7293 categories) or time-series data. This version also includes a randomised
7294 algorithm which is more efficient for larger data sets.")
7295 (license license:gpl3)))
7297 (define-public r-bicare
7304 (uri (bioconductor-uri "BicARE" version))
7307 "0llckbl3l26lf6wgjg7rxs8k1yrk043vvdhnkc6ncg33sydj383y"))))
7308 (properties `((upstream-name . "BicARE")))
7309 (build-system r-build-system)
7311 `(("r-biobase" ,r-biobase)
7312 ("r-gseabase" ,r-gseabase)
7313 ("r-multtest" ,r-multtest)))
7314 (home-page "http://bioinfo.curie.fr")
7315 (synopsis "Biclustering analysis and results exploration")
7317 "This is a package for biclustering analysis and exploration of
7319 (license license:gpl2)))
7321 (define-public r-bifet
7328 (uri (bioconductor-uri "BiFET" version))
7331 "1v2dshs09iy2glzq0vwxmr83x867j844i1ixsfcamvfq33fwbbr5"))))
7332 (properties `((upstream-name . "BiFET")))
7333 (build-system r-build-system)
7335 `(("r-genomicranges" ,r-genomicranges)
7336 ("r-poibin" ,r-poibin)))
7338 `(("r-knitr" ,r-knitr)))
7339 (home-page "https://bioconductor.org/packages/BiFET")
7340 (synopsis "Bias-free footprint enrichment test")
7342 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
7343 over-represented in target regions compared to background regions after
7344 correcting for the bias arising from the imbalance in read counts and GC
7345 contents between the target and background regions. For a given TF k, BiFET
7346 tests the null hypothesis that the target regions have the same probability of
7347 having footprints for the TF k as the background regions while correcting for
7348 the read count and GC content bias.")
7349 (license license:gpl3)))
7351 (define-public r-rsbml
7358 (uri (bioconductor-uri "rsbml" version))
7361 "1i1izznnwzrc6m7s3hblfff466icfvxl2gjdqaln8qfg9v87rslx"))))
7362 (properties `((upstream-name . "rsbml")))
7363 (build-system r-build-system)
7365 `(("libsbml" ,libsbml)
7368 `(("r-biocgenerics" ,r-biocgenerics)
7369 ("r-graph" ,r-graph)))
7371 `(("pkg-config" ,pkg-config)))
7372 (home-page "http://www.sbml.org")
7373 (synopsis "R support for SBML")
7375 "This package provides an R interface to libsbml for SBML parsing,
7376 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
7377 (license license:artistic2.0)))
7379 (define-public r-hypergraph
7381 (name "r-hypergraph")
7386 (uri (bioconductor-uri "hypergraph" version))
7389 "1iq9b9rzy3ikx8xszsjiv3p8l702n2h2s9w33797wcmkg4apslb7"))))
7390 (properties `((upstream-name . "hypergraph")))
7391 (build-system r-build-system)
7393 `(("r-graph" ,r-graph)))
7394 (home-page "https://bioconductor.org/packages/hypergraph")
7395 (synopsis "Hypergraph data structures")
7397 "This package implements some simple capabilities for representing and
7398 manipulating hypergraphs.")
7399 (license license:artistic2.0)))
7401 (define-public r-hyperdraw
7403 (name "r-hyperdraw")
7408 (uri (bioconductor-uri "hyperdraw" version))
7411 "1qzx5sqp7rpspk8g1j34p03ds1vmw0h7hpzb2ijpbvmsja5drzvf"))))
7412 (properties `((upstream-name . "hyperdraw")))
7413 (build-system r-build-system)
7414 (inputs `(("graphviz" ,graphviz)))
7416 `(("r-graph" ,r-graph)
7417 ("r-hypergraph" ,r-hypergraph)
7418 ("r-rgraphviz" ,r-rgraphviz)))
7419 (home-page "https://bioconductor.org/packages/hyperdraw")
7420 (synopsis "Visualizing hypergraphs")
7422 "This package provides functions for visualizing hypergraphs.")
7423 (license license:gpl2+)))
7425 (define-public r-biggr
7432 (uri (bioconductor-uri "BiGGR" version))
7435 "05afi6hsh1dv6lc6l0dfhvvi8k34wyzf1k1jimam7a6pbrhyy5dk"))))
7436 (properties `((upstream-name . "BiGGR")))
7437 (build-system r-build-system)
7439 `(("r-hyperdraw" ,r-hyperdraw)
7440 ("r-hypergraph" ,r-hypergraph)
7442 ("r-limsolve" ,r-limsolve)
7443 ("r-rsbml" ,r-rsbml)
7444 ("r-stringr" ,r-stringr)))
7445 (home-page "https://bioconductor.org/packages/BiGGR/")
7446 (synopsis "Constraint based modeling using metabolic reconstruction databases")
7448 "This package provides an interface to simulate metabolic reconstruction
7449 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
7450 reconstruction databases. The package facilitates @dfn{flux balance
7451 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
7452 networks and estimated fluxes can be visualized with hypergraphs.")
7453 (license license:gpl3+)))
7455 (define-public r-bigmemoryextras
7457 (name "r-bigmemoryextras")
7462 (uri (bioconductor-uri "bigmemoryExtras" version))
7465 "053bqcd3p4i7agj43ccjxfz40a1sxrymd49vdpfq8ypslkwk7g0g"))))
7467 `((upstream-name . "bigmemoryExtras")))
7468 (build-system r-build-system)
7470 `(("r-bigmemory" ,r-bigmemory)))
7472 `(("r-knitr" ,r-knitr)))
7473 (home-page "https://github.com/phaverty/bigmemoryExtras")
7474 (synopsis "Extension of the bigmemory package")
7476 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
7477 safety and convenience features to the @code{filebacked.big.matrix} class from
7478 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
7479 monitoring and gracefully restoring the connection to on-disk data and it also
7480 protects against accidental data modification with a filesystem-based
7481 permissions system. Utilities are provided for using @code{BigMatrix}-derived
7482 classes as @code{assayData} matrices within the @code{Biobase} package's
7483 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
7484 related to attaching to, and indexing into, file-backed matrices with
7485 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
7486 a file-backed matrix with factor properties.")
7487 (license license:artistic2.0)))
7489 (define-public r-bigpint
7496 (uri (bioconductor-uri "bigPint" version))
7499 "1m92ngkzimcc37byf0ziphrby8wmjd5hfa53gvfphgaakyj9bjg8"))))
7500 (properties `((upstream-name . "bigPint")))
7501 (build-system r-build-system)
7503 `(("r-delayedarray" ,r-delayedarray)
7504 ("r-dplyr" ,r-dplyr)
7505 ("r-ggally" ,r-ggally)
7506 ("r-ggplot2" ,r-ggplot2)
7507 ("r-gridextra" ,r-gridextra)
7508 ("r-hexbin" ,r-hexbin)
7509 ("r-hmisc" ,r-hmisc)
7510 ("r-htmlwidgets" ,r-htmlwidgets)
7511 ("r-plotly" ,r-plotly)
7513 ("r-rcolorbrewer" ,r-rcolorbrewer)
7514 ("r-reshape" ,r-reshape)
7515 ("r-shiny" ,r-shiny)
7516 ("r-shinycssloaders" ,r-shinycssloaders)
7517 ("r-shinydashboard" ,r-shinydashboard)
7518 ("r-stringr" ,r-stringr)
7519 ("r-summarizedexperiment" ,r-summarizedexperiment)
7520 ("r-tidyr" ,r-tidyr)))
7522 `(("r-knitr" ,r-knitr)))
7523 (home-page "https://github.com/lindsayrutter/bigPint")
7524 (synopsis "Big multivariate data plotted interactively")
7526 "This package provides methods for visualizing large multivariate
7527 datasets using static and interactive scatterplot matrices, parallel
7528 coordinate plots, volcano plots, and litre plots. It includes examples for
7529 visualizing RNA-sequencing datasets and differentially expressed genes.")
7530 (license license:gpl3)))
7532 (define-public r-chemminer
7534 (name "r-chemminer")
7539 (uri (bioconductor-uri "ChemmineR" version))
7542 "0cna5xsqflvhlp2k47asxyv3w4ympmz2wy2cwjyzlal6936fjikf"))))
7543 (properties `((upstream-name . "ChemmineR")))
7544 (build-system r-build-system)
7546 `(("r-base64enc" ,r-base64enc)
7548 ("r-biocgenerics" ,r-biocgenerics)
7550 ("r-digest" ,r-digest)
7552 ("r-ggplot2" ,r-ggplot2)
7553 ("r-gridextra" ,r-gridextra)
7556 ("r-rcurl" ,r-rcurl)
7557 ("r-rjson" ,r-rjson)
7558 ("r-rsvg" ,r-rsvg)))
7560 `(("r-knitr" ,r-knitr)))
7561 (home-page "https://github.com/girke-lab/ChemmineR")
7562 (synopsis "Cheminformatics toolkit for R")
7564 "ChemmineR is a cheminformatics package for analyzing drug-like small
7565 molecule data in R. It contains functions for efficient processing of large
7566 numbers of molecules, physicochemical/structural property predictions,
7567 structural similarity searching, classification and clustering of compound
7568 libraries with a wide spectrum of algorithms. In addition, it offers
7569 visualization functions for compound clustering results and chemical
7571 (license license:artistic2.0)))
7573 (define-public r-bioassayr
7575 (name "r-bioassayr")
7580 (uri (bioconductor-uri "bioassayR" version))
7583 "1n0gsnxcl0lplqk8rs5ygxrxpx389ddl6wv3ciyz9g2xry5biyfy"))))
7584 (properties `((upstream-name . "bioassayR")))
7585 (build-system r-build-system)
7587 `(("r-biocgenerics" ,r-biocgenerics)
7588 ("r-chemminer" ,r-chemminer)
7590 ("r-matrix" ,r-matrix)
7591 ("r-rjson" ,r-rjson)
7592 ("r-rsqlite" ,r-rsqlite)
7595 `(("r-knitr" ,r-knitr)))
7596 (home-page "https://github.com/TylerBackman/bioassayR")
7597 (synopsis "Cross-target analysis of small molecule bioactivity")
7599 "bioassayR is a computational tool that enables simultaneous analysis of
7600 thousands of bioassay experiments performed over a diverse set of compounds
7601 and biological targets. Unique features include support for large-scale
7602 cross-target analyses of both public and custom bioassays, generation of
7603 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
7604 preloaded database that provides access to a substantial portion of publicly
7605 available bioactivity data.")
7606 (license license:artistic2.0)))
7608 (define-public r-biobroom
7615 (uri (bioconductor-uri "biobroom" version))
7618 "06qcrprn58kbrr5kyw1jl6z88b9w9g8xs6rkhrbnz8k7rv373fhf"))))
7619 (properties `((upstream-name . "biobroom")))
7620 (build-system r-build-system)
7622 `(("r-biobase" ,r-biobase)
7623 ("r-broom" ,r-broom)
7624 ("r-dplyr" ,r-dplyr)
7625 ("r-tidyr" ,r-tidyr)))
7627 `(("r-knitr" ,r-knitr)))
7628 (home-page "https://github.com/StoreyLab/biobroom")
7629 (synopsis "Turn Bioconductor objects into tidy data frames")
7631 "This package contains methods for converting standard objects
7632 constructed by bioinformatics packages, especially those in Bioconductor, and
7633 converting them to @code{tidy} data. It thus serves as a complement to the
7634 @code{broom} package, and follows the same tidy, augment, glance division of
7635 tidying methods. Tidying data makes it easy to recombine, reshape and
7636 visualize bioinformatics analyses.")
7637 ;; Any version of the LGPL.
7638 (license license:lgpl3+)))
7640 (define-public r-graphite
7647 (uri (bioconductor-uri "graphite" version))
7650 "0rc9cw3picz1y0lwhbzpk03ciij8kij74m15qgzh2ykla7zprb2p"))))
7651 (properties `((upstream-name . "graphite")))
7652 (build-system r-build-system)
7654 `(("r-annotationdbi" ,r-annotationdbi)
7655 ("r-checkmate" ,r-checkmate)
7656 ("r-graph" ,r-graph)
7658 ("r-rappdirs" ,r-rappdirs)))
7659 (home-page "https://bioconductor.org/packages/graphite/")
7660 (synopsis "Networks from pathway databases")
7662 "Graphite provides networks derived from eight public pathway databases,
7663 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
7665 (license license:agpl3+)))
7667 (define-public r-reactomepa
7669 (name "r-reactomepa")
7674 (uri (bioconductor-uri "ReactomePA" version))
7677 "1ngilyn1mihwxs4sh5gk9y829xghdmh277cfw3vfgflz9sgwy21x"))))
7678 (properties `((upstream-name . "ReactomePA")))
7679 (build-system r-build-system)
7681 `(("r-annotationdbi" ,r-annotationdbi)
7683 ("r-enrichplot" ,r-enrichplot)
7684 ("r-ggplot2" ,r-ggplot2)
7685 ("r-ggraph" ,r-ggraph)
7686 ("r-graphite" ,r-graphite)
7687 ("r-igraph" ,r-igraph)
7688 ("r-reactome-db" ,r-reactome-db)))
7690 `(("r-knitr" ,r-knitr)))
7691 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
7692 (synopsis "Reactome pathway analysis")
7694 "This package provides functions for pathway analysis based on the
7695 REACTOME pathway database. It implements enrichment analysis, gene set
7696 enrichment analysis and several functions for visualization.")
7697 (license license:gpl2)))
7699 (define-public r-ebarrays
7706 (uri (bioconductor-uri "EBarrays" version))
7709 "00ld26bld8xgin9zqwxybahvhmqbrvr09jfphg0yr4j4zck6sqgf"))))
7710 (properties `((upstream-name . "EBarrays")))
7711 (build-system r-build-system)
7713 `(("r-biobase" ,r-biobase)
7714 ("r-cluster" ,r-cluster)
7715 ("r-lattice" ,r-lattice)))
7716 (home-page "https://bioconductor.org/packages/EBarrays/")
7717 (synopsis "Gene clustering and differential expression identification")
7719 "EBarrays provides tools for the analysis of replicated/unreplicated
7721 (license license:gpl2+)))
7723 (define-public r-bioccasestudies
7725 (name "r-bioccasestudies")
7730 (uri (bioconductor-uri "BiocCaseStudies" version))
7733 "0fadck1dk1zavpn9yrcwx6zgfi18fw5xfs8svgzipns6bq41j8ix"))))
7735 `((upstream-name . "BiocCaseStudies")))
7736 (build-system r-build-system)
7737 (propagated-inputs `(("r-biobase" ,r-biobase)))
7738 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
7739 (synopsis "Support for the case studies monograph")
7741 "This package provides software and data to support the case studies
7743 (license license:artistic2.0)))
7745 (define-public r-biocgraph
7747 (name "r-biocgraph")
7752 (uri (bioconductor-uri "biocGraph" version))
7755 "1372bm4y3czqhpki10pnprxfkfncfcsy59zzvf8wj6q03acaavrj"))))
7756 (properties `((upstream-name . "biocGraph")))
7757 (build-system r-build-system)
7759 `(("r-biocgenerics" ,r-biocgenerics)
7760 ("r-geneplotter" ,r-geneplotter)
7761 ("r-graph" ,r-graph)
7762 ("r-rgraphviz" ,r-rgraphviz)))
7763 (home-page "https://bioconductor.org/packages/biocGraph/")
7764 (synopsis "Graph examples and use cases in Bioinformatics")
7766 "This package provides examples and code that make use of the
7767 different graph related packages produced by Bioconductor.")
7768 (license license:artistic2.0)))
7770 (define-public r-experimenthub
7772 (name "r-experimenthub")
7777 (uri (bioconductor-uri "ExperimentHub" version))
7780 "1kgvprchz1fg8pl1irj62mk2gyb4jcc9iimpypv4c2iccy5bp84x"))))
7781 (properties `((upstream-name . "ExperimentHub")))
7782 (build-system r-build-system)
7784 `(("r-annotationhub" ,r-annotationhub)
7785 ("r-biocfilecache" ,r-biocfilecache)
7786 ("r-biocgenerics" ,r-biocgenerics)
7787 ("r-biocmanager" ,r-biocmanager)
7789 ("r-rappdirs" ,r-rappdirs)
7790 ("r-s4vectors" ,r-s4vectors)))
7792 `(("r-knitr" ,r-knitr)))
7793 (home-page "https://bioconductor.org/packages/ExperimentHub/")
7794 (synopsis "Client to access ExperimentHub resources")
7796 "This package provides a client for the Bioconductor ExperimentHub web
7797 resource. ExperimentHub provides a central location where curated data from
7798 experiments, publications or training courses can be accessed. Each resource
7799 has associated metadata, tags and date of modification. The client creates
7800 and manages a local cache of files retrieved enabling quick and reproducible
7802 (license license:artistic2.0)))
7804 (define-public r-multiassayexperiment
7806 (name "r-multiassayexperiment")
7811 (uri (bioconductor-uri "MultiAssayExperiment" version))
7814 "0qlfnd86999jqv2nd0ikixi2sfd449dyg3ml4nbs8ycs57c2irgh"))))
7816 `((upstream-name . "MultiAssayExperiment")))
7817 (build-system r-build-system)
7819 `(("r-biobase" ,r-biobase)
7820 ("r-biocgenerics" ,r-biocgenerics)
7821 ("r-genomicranges" ,r-genomicranges)
7822 ("r-iranges" ,r-iranges)
7823 ("r-s4vectors" ,r-s4vectors)
7824 ("r-summarizedexperiment" ,r-summarizedexperiment)
7825 ("r-tidyr" ,r-tidyr)))
7827 `(("r-knitr" ,r-knitr)))
7828 (home-page "https://waldronlab.io/MultiAssayExperiment/")
7829 (synopsis "Integration of multi-omics experiments in Bioconductor")
7831 "MultiAssayExperiment harmonizes data management of multiple assays
7832 performed on an overlapping set of specimens. It provides a familiar
7833 Bioconductor user experience by extending concepts from
7834 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
7835 classes for individual assays, and allowing subsetting by genomic ranges or
7837 (license license:artistic2.0)))
7839 (define-public r-bioconcotk
7841 (name "r-bioconcotk")
7846 (uri (bioconductor-uri "BiocOncoTK" version))
7849 "021qzygfwdnd3naz1iqq01zr3zxv3k7wm1lklik24vc7axshxbmk"))))
7850 (properties `((upstream-name . "BiocOncoTK")))
7851 (build-system r-build-system)
7853 `(("r-bigrquery" ,r-bigrquery)
7855 ("r-complexheatmap" ,r-complexheatmap)
7856 ("r-curatedtcgadata" ,r-curatedtcgadata)
7858 ("r-dplyr" ,r-dplyr)
7860 ("r-genomicfeatures" ,r-genomicfeatures)
7861 ("r-genomicranges" ,r-genomicranges)
7862 ("r-ggplot2" ,r-ggplot2)
7863 ("r-ggpubr" ,r-ggpubr)
7864 ("r-graph" ,r-graph)
7866 ("r-iranges" ,r-iranges)
7867 ("r-magrittr" ,r-magrittr)
7869 ("r-rgraphviz" ,r-rgraphviz)
7870 ("r-rjson" ,r-rjson)
7871 ("r-s4vectors" ,r-s4vectors)
7872 ("r-scales" ,r-scales)
7873 ("r-shiny" ,r-shiny)
7874 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7876 `(("r-knitr" ,r-knitr)))
7877 (home-page "https://bioconductor.org/packages/BiocOncoTK")
7878 (synopsis "Bioconductor components for general cancer genomics")
7880 "The purpose of this package is to provide a central interface to various
7881 tools for genome-scale analysis of cancer studies.")
7882 (license license:artistic2.0)))
7884 (define-public r-biocor
7891 (uri (bioconductor-uri "BioCor" version))
7894 "1xghclfqv8d23g72g8914br5zjx4sz9zihzczwwmpl15lghpnqwy"))))
7895 (properties `((upstream-name . "BioCor")))
7896 (build-system r-build-system)
7898 `(("r-biocparallel" ,r-biocparallel)
7899 ("r-gseabase" ,r-gseabase)
7900 ("r-matrix" ,r-matrix)))
7902 `(("r-knitr" ,r-knitr)))
7903 (home-page "https://llrs.github.io/BioCor/")
7904 (synopsis "Functional similarities")
7906 "This package provides tools to calculate functional similarities based
7907 on the pathways described on KEGG and REACTOME or in gene sets. These
7908 similarities can be calculated for pathways or gene sets, genes, or clusters
7909 and combined with other similarities. They can be used to improve networks,
7910 gene selection, testing relationships, and so on.")
7911 (license license:expat)))
7913 (define-public r-biocpkgtools
7915 (name "r-biocpkgtools")
7920 (uri (bioconductor-uri "BiocPkgTools" version))
7923 "0l5fvi1m4834n4h0iswbap135s9mpaiabw9czzn1r72ssz86vrcr"))))
7924 (properties `((upstream-name . "BiocPkgTools")))
7925 (build-system r-build-system)
7927 `(("r-biocfilecache" ,r-biocfilecache)
7928 ("r-biocmanager" ,r-biocmanager)
7929 ("r-biocviews" ,r-biocviews)
7930 ("r-dplyr" ,r-dplyr)
7933 ("r-graph" ,r-graph)
7934 ("r-htmltools" ,r-htmltools)
7935 ("r-htmlwidgets" ,r-htmlwidgets)
7937 ("r-igraph" ,r-igraph)
7938 ("r-jsonlite" ,r-jsonlite)
7939 ("r-magrittr" ,r-magrittr)
7940 ("r-rappdirs" ,r-rappdirs)
7942 ("r-readr" ,r-readr)
7944 ("r-rlang" ,r-rlang)
7945 ("r-rvest" ,r-rvest)
7946 ("r-stringr" ,r-stringr)
7947 ("r-tibble" ,r-tibble)
7948 ("r-tidyr" ,r-tidyr)
7949 ("r-tidyselect" ,r-tidyselect)
7950 ("r-xml2" ,r-xml2)))
7952 `(("r-knitr" ,r-knitr)))
7953 (home-page "https://github.com/seandavi/BiocPkgTools")
7954 (synopsis "Collection of tools for learning about Bioconductor packages")
7956 "Bioconductor has a rich ecosystem of metadata around packages, usage,
7957 and build status. This package is a simple collection of functions to access
7958 that metadata from R. The goal is to expose metadata for data mining and
7959 value-added functionality such as package searching, text mining, and
7960 analytics on packages.")
7961 (license license:expat)))
7963 (define-public r-biocset
7970 (uri (bioconductor-uri "BiocSet" version))
7973 "041hq3rp0kv7kjwcjjrksk8lw3sj6j1v3wdcr8z611k0g0z6p0cj"))))
7974 (properties `((upstream-name . "BiocSet")))
7975 (build-system r-build-system)
7977 `(("r-annotationdbi" ,r-annotationdbi)
7978 ("r-dplyr" ,r-dplyr)
7979 ("r-keggrest" ,r-keggrest)
7981 ("r-rlang" ,r-rlang)
7982 ("r-rtracklayer" ,r-rtracklayer)
7983 ("r-tibble" ,r-tibble)))
7985 `(("r-knitr" ,r-knitr)))
7987 "https://bioconductor.org/packages/BiocSet")
7989 "Representing Different Biological Sets")
7991 "BiocSet displays different biological sets in a triple tibble format.
7992 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
7993 The user has the ability to activate one of these three tibbles to perform
7994 common functions from the @code{dplyr} package. Mapping functionality and
7995 accessing web references for elements/sets are also available in BiocSet.")
7996 (license license:artistic2.0)))
7998 (define-public r-biocworkflowtools
8000 (name "r-biocworkflowtools")
8005 (uri (bioconductor-uri "BiocWorkflowTools" version))
8008 "0p9r71ql67sdlgd5pv118lhz8b85pr5y4ijfwzcy8wrr8jwlbddy"))))
8010 `((upstream-name . "BiocWorkflowTools")))
8011 (build-system r-build-system)
8013 `(("r-biocstyle" ,r-biocstyle)
8014 ("r-bookdown" ,r-bookdown)
8015 ("r-git2r" ,r-git2r)
8017 ("r-knitr" ,r-knitr)
8018 ("r-rmarkdown" ,r-rmarkdown)
8019 ("r-rstudioapi" ,r-rstudioapi)
8020 ("r-stringr" ,r-stringr)
8021 ("r-usethis" ,r-usethis)))
8023 `(("r-knitr" ,r-knitr)))
8024 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
8025 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
8027 "This package provides functions to ease the transition between
8028 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
8029 (license license:expat)))
8031 (define-public r-biodist
8038 (uri (bioconductor-uri "bioDist" version))
8041 "17bvxk0anvsp29j5nbblvaymf8qgbj3sz4ir2l7wj8kb8jfi19cp"))))
8042 (properties `((upstream-name . "bioDist")))
8043 (build-system r-build-system)
8045 `(("r-biobase" ,r-biobase)
8046 ("r-kernsmooth" ,r-kernsmooth)))
8047 (home-page "https://bioconductor.org/packages/bioDist/")
8048 (synopsis "Different distance measures")
8050 "This package provides a collection of software tools for calculating
8051 distance measures.")
8052 (license license:artistic2.0)))
8054 (define-public r-pcatools
8061 (uri (bioconductor-uri "PCAtools" version))
8064 "0mnwqrhm1hmhzwrpidf6z207w1ycpm572snvpp5swlg6hnxq6bnc"))))
8065 (properties `((upstream-name . "PCAtools")))
8066 (build-system r-build-system)
8068 `(("r-beachmat" ,r-beachmat)
8070 ("r-biocparallel" ,r-biocparallel)
8071 ("r-biocsingular" ,r-biocsingular)
8072 ("r-cowplot" ,r-cowplot)
8073 ("r-delayedarray" ,r-delayedarray)
8074 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8075 ("r-dqrng" ,r-dqrng)
8076 ("r-ggplot2" ,r-ggplot2)
8077 ("r-ggrepel" ,r-ggrepel)
8078 ("r-lattice" ,r-lattice)
8079 ("r-matrix" ,r-matrix)
8081 ("r-reshape2" ,r-reshape2)))
8082 (native-inputs `(("r-knitr" ,r-knitr)))
8083 (home-page "https://github.com/kevinblighe/PCAtools")
8084 (synopsis "PCAtools: everything Principal Components Analysis")
8086 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
8087 structure of the data without the need to build any model to represent it.
8088 This \"summary\" of the data is arrived at through a process of reduction that
8089 can transform the large number of variables into a lesser number that are
8090 uncorrelated (i.e. the 'principal components'), while at the same time being
8091 capable of easy interpretation on the original data. PCAtools provides
8092 functions for data exploration via PCA, and allows the user to generate
8093 publication-ready figures. PCA is performed via @code{BiocSingular}; users
8094 can also identify an optimal number of principal components via different
8095 metrics, such as the elbow method and Horn's parallel analysis, which has
8096 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
8097 dimensional mass cytometry data.")
8098 (license license:gpl3)))
8100 (define-public r-rgreat
8107 (uri (bioconductor-uri "rGREAT" version))
8110 "0n8dw9ibb2klsczcxvvinpi9l53w8cs436i0c8w2jmramayl593v"))))
8111 (properties `((upstream-name . "rGREAT")))
8112 (build-system r-build-system)
8114 `(("r-genomicranges" ,r-genomicranges)
8115 ("r-getoptlong" ,r-getoptlong)
8116 ("r-iranges" ,r-iranges)
8117 ("r-rcurl" ,r-rcurl)
8118 ("r-rjson" ,r-rjson)))
8119 (native-inputs `(("r-knitr" ,r-knitr)))
8120 (home-page "https://github.com/jokergoo/rGREAT")
8121 (synopsis "Client for GREAT analysis")
8123 "This package makes GREAT (Genomic Regions Enrichment of Annotations
8124 Tool) analysis automatic by constructing a HTTP POST request according to
8125 user's input and automatically retrieving results from GREAT web server.")
8126 (license license:expat)))
8128 (define-public r-m3c
8135 (uri (bioconductor-uri "M3C" version))
8138 "0zq8lm4280p8h65i7myscwa4srs5ajh944xv6zni2f5sjyp7ij2y"))))
8139 (properties `((upstream-name . "M3C")))
8140 (build-system r-build-system)
8142 `(("r-cluster" ,r-cluster)
8143 ("r-corpcor" ,r-corpcor)
8144 ("r-doparallel" ,r-doparallel)
8145 ("r-dosnow" ,r-dosnow)
8146 ("r-foreach" ,r-foreach)
8147 ("r-ggplot2" ,r-ggplot2)
8148 ("r-matrix" ,r-matrix)
8149 ("r-matrixcalc" ,r-matrixcalc)
8150 ("r-rtsne" ,r-rtsne)
8151 ("r-umap" ,r-umap)))
8152 (native-inputs `(("r-knitr" ,r-knitr)))
8153 (home-page "https://bioconductor.org/packages/M3C")
8154 (synopsis "Monte Carlo reference-based consensus clustering")
8156 "M3C is a consensus clustering algorithm that uses a Monte Carlo
8157 simulation to eliminate overestimation of @code{K} and can reject the null
8158 hypothesis @code{K=1}.")
8159 (license license:agpl3+)))
8161 (define-public r-icens
8168 (uri (bioconductor-uri "Icens" version))
8171 "0fh7wgkrw20f61p06i87nccnbig9wv4m0jcg7cx1rw7g2ndnabgp"))))
8172 (properties `((upstream-name . "Icens")))
8173 (build-system r-build-system)
8175 `(("r-survival" ,r-survival)))
8176 (home-page "https://bioconductor.org/packages/Icens")
8177 (synopsis "NPMLE for censored and truncated data")
8179 "This package provides many functions for computing the
8180 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
8182 (license license:artistic2.0)))
8184 ;; This is a CRAN package but it depends on r-icens, which is published on
8186 (define-public r-interval
8193 (uri (cran-uri "interval" version))
8196 "1lln9jkli28i4wivwzqrsxvv2n15560f7msjy5gssrm45vxrxms8"))))
8197 (properties `((upstream-name . "interval")))
8198 (build-system r-build-system)
8200 `(("r-icens" ,r-icens)
8201 ("r-mlecens" ,r-mlecens)
8203 ("r-survival" ,r-survival)))
8204 (home-page "https://cran.r-project.org/web/packages/interval/")
8205 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
8207 "This package provides functions to fit nonparametric survival curves,
8208 plot them, and perform logrank or Wilcoxon type tests.")
8209 (license license:gpl2+)))
8211 ;; This is a CRAN package, but it depends on r-interval, which depends on a
8212 ;; Bioconductor package.
8213 (define-public r-fhtest
8220 (uri (cran-uri "FHtest" version))
8223 "1wsn0j9ydpp9nfswiqg21p09kgkvaq8fh0y0h8syqgizah7i8vs2"))))
8224 (properties `((upstream-name . "FHtest")))
8225 (build-system r-build-system)
8227 `(("r-interval" ,r-interval)
8228 ("r-kmsurv" ,r-kmsurv)
8231 ("r-survival" ,r-survival)))
8232 (home-page "https://cran.r-project.org/web/packages/FHtest/")
8233 (synopsis "Tests for survival data based on the Fleming-Harrington class")
8235 "This package provides functions to compare two or more survival curves
8239 @item The Fleming-Harrington test for right-censored data based on
8240 permutations and on counting processes.
8241 @item An extension of the Fleming-Harrington test for interval-censored data
8242 based on a permutation distribution and on a score vector distribution.
8245 (license license:gpl2+)))
8247 (define-public r-fourcseq
8254 (uri (bioconductor-uri "FourCSeq" version))
8256 (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
8257 (properties `((upstream-name . "FourCSeq")))
8258 (build-system r-build-system)
8260 `(("r-biobase" ,r-biobase)
8261 ("r-biostrings" ,r-biostrings)
8262 ("r-deseq2" ,r-deseq2)
8264 ("r-genomicalignments" ,r-genomicalignments)
8265 ("r-genomicranges" ,r-genomicranges)
8266 ("r-ggbio" ,r-ggbio)
8267 ("r-ggplot2" ,r-ggplot2)
8268 ("r-gtools" ,r-gtools)
8270 ("r-matrix" ,r-matrix)
8271 ("r-reshape2" ,r-reshape2)
8272 ("r-rsamtools" ,r-rsamtools)
8273 ("r-rtracklayer" ,r-rtracklayer)
8274 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8276 `(("r-knitr" ,r-knitr)))
8278 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
8279 (synopsis "Analysis of multiplexed 4C sequencing data")
8281 "This package is an R package dedicated to the analysis of (multiplexed)
8282 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
8283 interactions between DNA elements and identify differential interactions
8284 between conditions. The statistical analysis in R starts with individual bam
8285 files for each sample as inputs. To obtain these files, the package contains
8286 a Python script to demultiplex libraries and trim off primer sequences. With
8287 a standard alignment software the required bam files can be then be
8289 (license license:gpl3+)))
8291 (define-public r-preprocesscore
8293 (name "r-preprocesscore")
8298 (uri (bioconductor-uri "preprocessCore" version))
8301 "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl"))))
8303 `((upstream-name . "preprocessCore")))
8304 (build-system r-build-system)
8305 (home-page "https://github.com/bmbolstad/preprocessCore")
8306 (synopsis "Collection of pre-processing functions")
8308 "This package provides a library of core pre-processing and normalization
8310 (license license:lgpl2.0+)))
8312 (define-public r-rgraphviz
8314 (name "r-rgraphviz")
8319 (uri (bioconductor-uri "Rgraphviz" version))
8322 "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y"))))
8323 (properties `((upstream-name . "Rgraphviz")))
8324 (build-system r-build-system)
8327 (modify-phases %standard-phases
8328 (add-after 'unpack 'make-reproducible
8330 ;; The replacement value is taken from src/graphviz/builddate.h
8331 (substitute* "src/graphviz/configure"
8332 (("VERSION_DATE=.*")
8333 "VERSION_DATE=20200427.2341\n"))
8335 ;; FIXME: Rgraphviz bundles the sources of an older variant of
8336 ;; graphviz. It does not build with the latest version of graphviz, so
8337 ;; we do not add graphviz to the inputs.
8338 (inputs `(("zlib" ,zlib)))
8340 `(("r-graph" ,r-graph)))
8342 `(("pkg-config" ,pkg-config)))
8343 (home-page "https://bioconductor.org/packages/Rgraphviz")
8344 (synopsis "Plotting capabilities for R graph objects")
8346 "This package interfaces R with the graphviz library for plotting R graph
8347 objects from the @code{graph} package.")
8348 (license license:epl1.0)))