1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
6 ;;; This file is part of GNU Guix.
8 ;;; GNU Guix is free software; you can redistribute it and/or modify it
9 ;;; under the terms of the GNU General Public License as published by
10 ;;; the Free Software Foundation; either version 3 of the License, or (at
11 ;;; your option) any later version.
13 ;;; GNU Guix is distributed in the hope that it will be useful, but
14 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
15 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16 ;;; GNU General Public License for more details.
18 ;;; You should have received a copy of the GNU General Public License
19 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
21 (define-module (gnu packages bioconductor)
22 #:use-module ((guix licenses) #:prefix license:)
23 #:use-module (guix packages)
24 #:use-module (guix download)
25 #:use-module (guix git-download)
26 #:use-module (guix build-system r)
27 #:use-module (gnu packages)
28 #:use-module (gnu packages base)
29 #:use-module (gnu packages bioinformatics)
30 #:use-module (gnu packages cran)
31 #:use-module (gnu packages compression)
32 #:use-module (gnu packages gcc)
33 #:use-module (gnu packages graph)
34 #:use-module (gnu packages haskell)
35 #:use-module (gnu packages image)
36 #:use-module (gnu packages maths)
37 #:use-module (gnu packages netpbm)
38 #:use-module (gnu packages perl)
39 #:use-module (gnu packages pkg-config)
40 #:use-module (gnu packages statistics)
41 #:use-module (gnu packages web)
42 #:use-module (srfi srfi-1))
47 (define-public r-bsgenome-celegans-ucsc-ce6
49 (name "r-bsgenome-celegans-ucsc-ce6")
53 ;; We cannot use bioconductor-uri here because this tarball is
54 ;; located under "data/annotation/" instead of "bioc/".
55 (uri (string-append "https://www.bioconductor.org/packages/"
56 "release/data/annotation/src/contrib/"
57 "BSgenome.Celegans.UCSC.ce6_"
61 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
63 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
64 (build-system r-build-system)
65 ;; As this package provides little more than a very large data file it
66 ;; doesn't make sense to build substitutes.
67 (arguments `(#:substitutable? #f))
69 `(("r-bsgenome" ,r-bsgenome)))
71 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
72 (synopsis "Full genome sequences for Worm")
74 "This package provides full genome sequences for Caenorhabditis
75 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
77 (license license:artistic2.0)))
79 (define-public r-bsgenome-celegans-ucsc-ce10
81 (name "r-bsgenome-celegans-ucsc-ce10")
85 ;; We cannot use bioconductor-uri here because this tarball is
86 ;; located under "data/annotation/" instead of "bioc/".
87 (uri (string-append "https://www.bioconductor.org/packages/"
88 "release/data/annotation/src/contrib/"
89 "BSgenome.Celegans.UCSC.ce10_"
93 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
95 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
96 (build-system r-build-system)
97 ;; As this package provides little more than a very large data file it
98 ;; doesn't make sense to build substitutes.
99 (arguments `(#:substitutable? #f))
101 `(("r-bsgenome" ,r-bsgenome)))
103 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
104 (synopsis "Full genome sequences for Worm")
106 "This package provides full genome sequences for Caenorhabditis
107 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
109 (license license:artistic2.0)))
111 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
113 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
117 ;; We cannot use bioconductor-uri here because this tarball is
118 ;; located under "data/annotation/" instead of "bioc/".
119 (uri (string-append "https://www.bioconductor.org/packages/"
120 "release/data/annotation/src/contrib/"
121 "BSgenome.Dmelanogaster.UCSC.dm6_"
125 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
127 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
128 (build-system r-build-system)
129 ;; As this package provides little more than a very large data file it
130 ;; doesn't make sense to build substitutes.
131 (arguments `(#:substitutable? #f))
133 `(("r-bsgenome" ,r-bsgenome)))
135 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
136 (synopsis "Full genome sequences for Fly")
138 "This package provides full genome sequences for Drosophila
139 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
141 (license license:artistic2.0)))
143 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
145 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
149 ;; We cannot use bioconductor-uri here because this tarball is
150 ;; located under "data/annotation/" instead of "bioc/".
151 (uri (string-append "https://www.bioconductor.org/packages/"
152 "release/data/annotation/src/contrib/"
153 "BSgenome.Dmelanogaster.UCSC.dm3_"
157 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
159 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
160 (build-system r-build-system)
161 ;; As this package provides little more than a very large data file it
162 ;; doesn't make sense to build substitutes.
163 (arguments `(#:substitutable? #f))
165 `(("r-bsgenome" ,r-bsgenome)))
167 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
168 (synopsis "Full genome sequences for Fly")
170 "This package provides full genome sequences for Drosophila
171 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
172 Biostrings objects.")
173 (license license:artistic2.0)))
175 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
177 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
181 ;; We cannot use bioconductor-uri here because this tarball is
182 ;; located under "data/annotation/" instead of "bioc/".
183 (uri (string-append "http://www.bioconductor.org/packages/"
184 "release/data/annotation/src/contrib/"
185 "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
189 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
191 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
192 (build-system r-build-system)
194 `(("r-bsgenome" ,r-bsgenome)
195 ("r-bsgenome-dmelanogaster-ucsc-dm3"
196 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
197 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
198 (synopsis "Full masked genome sequences for Fly")
200 "This package provides full masked genome sequences for Drosophila
201 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
202 Biostrings objects. The sequences are the same as in
203 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
204 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
205 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
206 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
207 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
208 (license license:artistic2.0)))
210 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
212 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
216 ;; We cannot use bioconductor-uri here because this tarball is
217 ;; located under "data/annotation/" instead of "bioc/".
218 (uri (string-append "https://www.bioconductor.org/packages/"
219 "release/data/annotation/src/contrib/"
220 "BSgenome.Hsapiens.1000genomes.hs37d5_"
224 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
226 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
227 (build-system r-build-system)
228 ;; As this package provides little more than a very large data file it
229 ;; doesn't make sense to build substitutes.
230 (arguments `(#:substitutable? #f))
232 `(("r-bsgenome" ,r-bsgenome)))
234 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
235 (synopsis "Full genome sequences for Homo sapiens")
237 "This package provides full genome sequences for Homo sapiens from
238 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
239 (license license:artistic2.0)))
241 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
243 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
247 ;; We cannot use bioconductor-uri here because this tarball is
248 ;; located under "data/annotation/" instead of "bioc/".
249 (uri (string-append "http://www.bioconductor.org/packages/"
250 "release/data/annotation/src/contrib/"
251 "BSgenome.Hsapiens.UCSC.hg19.masked_"
255 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
257 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
258 (build-system r-build-system)
260 `(("r-bsgenome" ,r-bsgenome)
261 ("r-bsgenome-hsapiens-ucsc-hg19"
262 ,r-bsgenome-hsapiens-ucsc-hg19)))
263 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
264 (synopsis "Full masked genome sequences for Homo sapiens")
266 "This package provides full genome sequences for Homo sapiens (Human) as
267 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
268 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
269 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
270 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
271 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
272 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
274 (license license:artistic2.0)))
276 (define-public r-bsgenome-mmusculus-ucsc-mm9
278 (name "r-bsgenome-mmusculus-ucsc-mm9")
282 ;; We cannot use bioconductor-uri here because this tarball is
283 ;; located under "data/annotation/" instead of "bioc/".
284 (uri (string-append "https://www.bioconductor.org/packages/"
285 "release/data/annotation/src/contrib/"
286 "BSgenome.Mmusculus.UCSC.mm9_"
290 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
292 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
293 (build-system r-build-system)
294 ;; As this package provides little more than a very large data file it
295 ;; doesn't make sense to build substitutes.
296 (arguments `(#:substitutable? #f))
298 `(("r-bsgenome" ,r-bsgenome)))
300 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
301 (synopsis "Full genome sequences for Mouse")
303 "This package provides full genome sequences for Mus musculus (Mouse) as
304 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
305 (license license:artistic2.0)))
307 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
309 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
313 ;; We cannot use bioconductor-uri here because this tarball is
314 ;; located under "data/annotation/" instead of "bioc/".
315 (uri (string-append "http://www.bioconductor.org/packages/"
316 "release/data/annotation/src/contrib/"
317 "BSgenome.Mmusculus.UCSC.mm9.masked_"
321 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
323 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
324 (build-system r-build-system)
326 `(("r-bsgenome" ,r-bsgenome)
327 ("r-bsgenome-mmusculus-ucsc-mm9"
328 ,r-bsgenome-mmusculus-ucsc-mm9)))
329 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
330 (synopsis "Full masked genome sequences for Mouse")
332 "This package provides full genome sequences for Mus musculus (Mouse) as
333 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
334 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
335 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
336 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
337 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
338 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
340 (license license:artistic2.0)))
342 (define-public r-bsgenome-mmusculus-ucsc-mm10
344 (name "r-bsgenome-mmusculus-ucsc-mm10")
348 ;; We cannot use bioconductor-uri here because this tarball is
349 ;; located under "data/annotation/" instead of "bioc/".
350 (uri (string-append "https://www.bioconductor.org/packages/"
351 "release/data/annotation/src/contrib/"
352 "BSgenome.Mmusculus.UCSC.mm10_"
356 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
358 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
359 (build-system r-build-system)
360 ;; As this package provides little more than a very large data file it
361 ;; doesn't make sense to build substitutes.
362 (arguments `(#:substitutable? #f))
364 `(("r-bsgenome" ,r-bsgenome)))
366 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
367 (synopsis "Full genome sequences for Mouse")
369 "This package provides full genome sequences for Mus
370 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
371 in Biostrings objects.")
372 (license license:artistic2.0)))
374 (define-public r-org-ce-eg-db
376 (name "r-org-ce-eg-db")
380 ;; We cannot use bioconductor-uri here because this tarball is
381 ;; located under "data/annotation/" instead of "bioc/".
382 (uri (string-append "https://www.bioconductor.org/packages/"
383 "release/data/annotation/src/contrib/"
384 "org.Ce.eg.db_" version ".tar.gz"))
387 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
389 `((upstream-name . "org.Ce.eg.db")))
390 (build-system r-build-system)
392 `(("r-annotationdbi" ,r-annotationdbi)))
393 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
394 (synopsis "Genome wide annotation for Worm")
396 "This package provides mappings from Entrez gene identifiers to various
397 annotations for the genome of the model worm Caenorhabditis elegans.")
398 (license license:artistic2.0)))
400 (define-public r-org-dm-eg-db
402 (name "r-org-dm-eg-db")
406 ;; We cannot use bioconductor-uri here because this tarball is
407 ;; located under "data/annotation/" instead of "bioc/".
408 (uri (string-append "https://www.bioconductor.org/packages/"
409 "release/data/annotation/src/contrib/"
410 "org.Dm.eg.db_" version ".tar.gz"))
413 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
415 `((upstream-name . "org.Dm.eg.db")))
416 (build-system r-build-system)
418 `(("r-annotationdbi" ,r-annotationdbi)))
419 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
420 (synopsis "Genome wide annotation for Fly")
422 "This package provides mappings from Entrez gene identifiers to various
423 annotations for the genome of the model fruit fly Drosophila melanogaster.")
424 (license license:artistic2.0)))
426 (define-public r-org-dr-eg-db
428 (name "r-org-dr-eg-db")
432 ;; We cannot use bioconductor-uri here because this tarball is
433 ;; located under "data/annotation/" instead of "bioc/".
434 (uri (string-append "https://www.bioconductor.org/packages/"
435 "release/data/annotation/src/contrib/"
436 "org.Dr.eg.db_" version ".tar.gz"))
439 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
441 `((upstream-name . "org.Dr.eg.db")))
442 (build-system r-build-system)
444 `(("r-annotationdbi" ,r-annotationdbi)))
445 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
446 (synopsis "Annotation for Zebrafish")
448 "This package provides genome wide annotations for Zebrafish, primarily
449 based on mapping using Entrez Gene identifiers.")
450 (license license:artistic2.0)))
452 (define-public r-org-hs-eg-db
454 (name "r-org-hs-eg-db")
458 ;; We cannot use bioconductor-uri here because this tarball is
459 ;; located under "data/annotation/" instead of "bioc/".
460 (uri (string-append "https://www.bioconductor.org/packages/"
461 "release/data/annotation/src/contrib/"
462 "org.Hs.eg.db_" version ".tar.gz"))
465 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
467 `((upstream-name . "org.Hs.eg.db")))
468 (build-system r-build-system)
470 `(("r-annotationdbi" ,r-annotationdbi)))
471 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
472 (synopsis "Genome wide annotation for Human")
474 "This package contains genome-wide annotations for Human, primarily based
475 on mapping using Entrez Gene identifiers.")
476 (license license:artistic2.0)))
478 (define-public r-org-mm-eg-db
480 (name "r-org-mm-eg-db")
484 ;; We cannot use bioconductor-uri here because this tarball is
485 ;; located under "data/annotation/" instead of "bioc/".
486 (uri (string-append "https://www.bioconductor.org/packages/"
487 "release/data/annotation/src/contrib/"
488 "org.Mm.eg.db_" version ".tar.gz"))
491 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
493 `((upstream-name . "org.Mm.eg.db")))
494 (build-system r-build-system)
496 `(("r-annotationdbi" ,r-annotationdbi)))
497 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
498 (synopsis "Genome wide annotation for Mouse")
500 "This package provides mappings from Entrez gene identifiers to various
501 annotations for the genome of the model mouse Mus musculus.")
502 (license license:artistic2.0)))
504 (define-public r-bsgenome-hsapiens-ucsc-hg19
506 (name "r-bsgenome-hsapiens-ucsc-hg19")
510 ;; We cannot use bioconductor-uri here because this tarball is
511 ;; located under "data/annotation/" instead of "bioc/".
512 (uri (string-append "https://www.bioconductor.org/packages/"
513 "release/data/annotation/src/contrib/"
514 "BSgenome.Hsapiens.UCSC.hg19_"
518 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
520 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
521 (build-system r-build-system)
522 ;; As this package provides little more than a very large data file it
523 ;; doesn't make sense to build substitutes.
524 (arguments `(#:substitutable? #f))
526 `(("r-bsgenome" ,r-bsgenome)))
528 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
529 (synopsis "Full genome sequences for Homo sapiens")
531 "This package provides full genome sequences for Homo sapiens as provided
532 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
533 (license license:artistic2.0)))
535 (define-public r-genelendatabase
537 (name "r-genelendatabase")
542 ;; We cannot use bioconductor-uri here because this tarball is
543 ;; located under "data/experiment/" instead of "bioc/".
544 (uri (string-append "https://bioconductor.org/packages/"
545 "release/data/experiment/src/contrib"
546 "/geneLenDataBase_" version ".tar.gz"))
549 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
551 `((upstream-name . "geneLenDataBase")))
552 (build-system r-build-system)
554 `(("r-rtracklayer" ,r-rtracklayer)
555 ("r-genomicfeatures" ,r-genomicfeatures)))
556 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
557 (synopsis "Lengths of mRNA transcripts for a number of genomes")
559 "This package provides the lengths of mRNA transcripts for a number of
560 genomes and gene ID formats, largely based on the UCSC table browser.")
561 (license license:lgpl2.0+)))
563 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
565 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
569 ;; We cannot use bioconductor-uri here because this tarball is
570 ;; located under "data/annotation/" instead of "bioc/".
571 (uri (string-append "https://bioconductor.org/packages/"
572 "release/data/annotation/src/contrib"
573 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
577 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
579 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
580 (build-system r-build-system)
581 ;; As this package provides little more than a very large data file it
582 ;; doesn't make sense to build substitutes.
583 (arguments `(#:substitutable? #f))
585 `(("r-genomicfeatures" ,r-genomicfeatures)))
587 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
588 (synopsis "Annotation package for human genome in TxDb format")
590 "This package provides an annotation database of Homo sapiens genome
591 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
592 track. The database is exposed as a @code{TxDb} object.")
593 (license license:artistic2.0)))
595 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
597 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
601 ;; We cannot use bioconductor-uri here because this tarball is
602 ;; located under "data/annotation/" instead of "bioc/".
603 (uri (string-append "https://bioconductor.org/packages/"
604 "release/data/annotation/src/contrib"
605 "/TxDb.Hsapiens.UCSC.hg38.knownGene_"
609 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
611 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
612 (build-system r-build-system)
614 `(("r-genomicfeatures" ,r-genomicfeatures)))
616 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
617 (synopsis "Annotation package for human genome in TxDb format")
619 "This package provides an annotation database of Homo sapiens genome
620 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
621 track. The database is exposed as a @code{TxDb} object.")
622 (license license:artistic2.0)))
624 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
626 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
630 ;; We cannot use bioconductor-uri here because this tarball is
631 ;; located under "data/annotation/" instead of "bioc/".
632 (uri (string-append "https://bioconductor.org/packages/"
633 "release/data/annotation/src/contrib"
634 "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
638 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
640 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
641 (build-system r-build-system)
643 `(("r-genomicfeatures" ,r-genomicfeatures)
644 ("r-annotationdbi" ,r-annotationdbi)))
646 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
647 (synopsis "Annotation package for mouse genome in TxDb format")
649 "This package provides an annotation database of Mouse genome data. It
650 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
651 database is exposed as a @code{TxDb} object.")
652 (license license:artistic2.0)))
654 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
656 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
660 ;; We cannot use bioconductor-uri here because this tarball is
661 ;; located under "data/annotation/" instead of "bioc/".
662 (uri (string-append "https://www.bioconductor.org/packages/"
663 "release/data/annotation/src/contrib/"
664 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
668 "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
670 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
671 (build-system r-build-system)
672 ;; As this package provides little more than a very large data file it
673 ;; doesn't make sense to build substitutes.
674 (arguments `(#:substitutable? #f))
676 `(("r-bsgenome" ,r-bsgenome)
677 ("r-genomicfeatures" ,r-genomicfeatures)
678 ("r-annotationdbi" ,r-annotationdbi)))
680 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
681 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
683 "This package loads a TxDb object, which is an R interface to
684 prefabricated databases contained in this package. This package provides
685 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
686 based on the knownGene track.")
687 (license license:artistic2.0)))
689 (define-public r-fdb-infiniummethylation-hg19
691 (name "r-fdb-infiniummethylation-hg19")
695 ;; We cannot use bioconductor-uri here because this tarball is
696 ;; located under "data/annotation/" instead of "bioc/".
697 (uri (string-append "https://www.bioconductor.org/packages/"
698 "release/data/annotation/src/contrib/"
699 "FDb.InfiniumMethylation.hg19_"
703 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
705 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
706 (build-system r-build-system)
708 `(("r-biostrings" ,r-biostrings)
709 ("r-genomicfeatures" ,r-genomicfeatures)
710 ("r-annotationdbi" ,r-annotationdbi)
711 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
712 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
713 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
714 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
716 "This is an annotation package for Illumina Infinium DNA methylation
717 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
719 (license license:artistic2.0)))
721 (define-public r-illuminahumanmethylationepicmanifest
723 (name "r-illuminahumanmethylationepicmanifest")
727 ;; We cannot use bioconductor-uri here because this tarball is
728 ;; located under "data/annotation/" instead of "bioc/".
729 (uri (string-append "https://www.bioconductor.org/packages/"
730 "release/data/annotation/src/contrib/"
731 "IlluminaHumanMethylationEPICmanifest_"
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-do-db
753 ;; We cannot use bioconductor-uri here because this tarball is
754 ;; located under "data/annotation/" instead of "bioc/".
755 (uri (string-append "https://www.bioconductor.org/packages/"
756 "release/data/annotation/src/contrib/"
757 "DO.db_" version ".tar.gz"))
760 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
762 `((upstream-name . "DO.db")))
763 (build-system r-build-system)
765 `(("r-annotationdbi" ,r-annotationdbi)))
766 (home-page "https://www.bioconductor.org/packages/DO.db/")
767 (synopsis "Annotation maps describing the entire Disease Ontology")
769 "This package provides a set of annotation maps describing the entire
771 (license license:artistic2.0)))
776 (define-public r-abadata
782 ;; We cannot use bioconductor-uri here because this tarball is
783 ;; located under "data/experiment/" instead of "bioc/".
784 (uri (string-append "https://www.bioconductor.org/packages/"
785 "release/data/experiment/src/contrib/"
786 "ABAData_" version ".tar.gz"))
789 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
791 `((upstream-name . "ABAData")))
792 (build-system r-build-system)
794 `(("r-annotationdbi" ,r-annotationdbi)))
795 (home-page "https://www.bioconductor.org/packages/ABAData/")
796 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
798 "This package provides the data for the gene expression enrichment
799 analysis conducted in the package ABAEnrichment. The package includes three
800 datasets which are derived from the Allen Brain Atlas:
803 @item Gene expression data from Human Brain (adults) averaged across donors,
804 @item Gene expression data from the Developing Human Brain pooled into five
805 age categories and averaged across donors, and
806 @item a developmental effect score based on the Developing Human Brain
810 All datasets are restricted to protein coding genes.")
811 (license license:gpl2+)))
813 (define-public r-arrmdata
819 ;; We cannot use bioconductor-uri here because this tarball is
820 ;; located under "data/experiment/" instead of "bioc/".
821 (uri (string-append "https://www.bioconductor.org/packages/"
822 "release/data/experiment/src/contrib/"
823 "ARRmData_" version ".tar.gz"))
826 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
828 `((upstream-name . "ARRmData")))
829 (build-system r-build-system)
830 (home-page "https://www.bioconductor.org/packages/ARRmData/")
831 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
833 "This package provides raw beta values from 36 samples across 3 groups
834 from Illumina 450k methylation arrays.")
835 (license license:artistic2.0)))
837 (define-public r-hsmmsinglecell
839 (name "r-hsmmsinglecell")
843 ;; We cannot use bioconductor-uri here because this tarball is
844 ;; located under "data/experiment/" instead of "bioc/".
845 (uri (string-append "https://www.bioconductor.org/packages/"
846 "release/data/experiment/src/contrib/"
847 "HSMMSingleCell_" version ".tar.gz"))
850 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
852 `((upstream-name . "HSMMSingleCell")))
853 (build-system r-build-system)
854 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
855 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
857 "Skeletal myoblasts undergo a well-characterized sequence of
858 morphological and transcriptional changes during differentiation. In this
859 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
860 under high mitogen conditions (GM) and then differentiated by switching to
861 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
862 hundred cells taken over a time-course of serum-induced differentiation.
863 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
864 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
865 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
866 which were then sequenced to a depth of ~4 million reads per library,
867 resulting in a complete gene expression profile for each cell.")
868 (license license:artistic2.0)))
876 ;; We cannot use bioconductor-uri here because this tarball is
877 ;; located under "data/experiment/" instead of "bioc/".
878 (uri (string-append "https://www.bioconductor.org/packages/"
879 "release/data/experiment/src/contrib/"
880 "ALL_" version ".tar.gz"))
883 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
884 (properties `((upstream-name . "ALL")))
885 (build-system r-build-system)
887 `(("r-biobase" ,r-biobase)))
888 (home-page "https://bioconductor.org/packages/ALL")
889 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
891 "The data consist of microarrays from 128 different individuals with
892 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
893 are available. The data have been normalized (using rma) and it is the
894 jointly normalized data that are available here. The data are presented in
895 the form of an @code{exprSet} object.")
896 (license license:artistic2.0)))
901 (define-public r-biocgenerics
903 (name "r-biocgenerics")
907 (uri (bioconductor-uri "BiocGenerics" version))
910 "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f"))))
912 `((upstream-name . "BiocGenerics")))
913 (build-system r-build-system)
914 (home-page "https://bioconductor.org/packages/BiocGenerics")
915 (synopsis "S4 generic functions for Bioconductor")
917 "This package provides S4 generic functions needed by many Bioconductor
919 (license license:artistic2.0)))
921 (define-public r-annotate
928 (uri (bioconductor-uri "annotate" version))
931 "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs"))))
932 (build-system r-build-system)
934 `(("r-annotationdbi" ,r-annotationdbi)
935 ("r-biobase" ,r-biobase)
936 ("r-biocgenerics" ,r-biocgenerics)
940 ("r-xtable" ,r-xtable)))
942 "https://bioconductor.org/packages/annotate")
943 (synopsis "Annotation for microarrays")
944 (description "This package provides R environments for the annotation of
946 (license license:artistic2.0)))
948 (define-public r-hpar
955 (uri (bioconductor-uri "hpar" version))
958 "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5"))))
959 (build-system r-build-system)
960 (home-page "https://bioconductor.org/packages/hpar/")
961 (synopsis "Human Protein Atlas in R")
962 (description "This package provides a simple interface to and data from
963 the Human Protein Atlas project.")
964 (license license:artistic2.0)))
966 (define-public r-regioner
973 (uri (bioconductor-uri "regioneR" version))
976 "1b8ybx4wcxlqw9nvajawsf0lqaqn9v89rxcawg4g3dbzlfssfc5q"))))
977 (properties `((upstream-name . "regioneR")))
978 (build-system r-build-system)
980 `(("r-biostrings" ,r-biostrings)
981 ("r-bsgenome" ,r-bsgenome)
982 ("r-genomeinfodb" ,r-genomeinfodb)
983 ("r-genomicranges" ,r-genomicranges)
984 ("r-iranges" ,r-iranges)
985 ("r-memoise" ,r-memoise)
986 ("r-rtracklayer" ,r-rtracklayer)
987 ("r-s4vectors" ,r-s4vectors)))
988 (home-page "https://bioconductor.org/packages/regioneR/")
989 (synopsis "Association analysis of genomic regions")
990 (description "This package offers a statistical framework based on
991 customizable permutation tests to assess the association between genomic
992 region sets and other genomic features.")
993 (license license:artistic2.0)))
995 (define-public r-geneplotter
997 (name "r-geneplotter")
1002 (uri (bioconductor-uri "geneplotter" version))
1005 "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb"))))
1006 (build-system r-build-system)
1008 `(("r-annotate" ,r-annotate)
1009 ("r-annotationdbi" ,r-annotationdbi)
1010 ("r-biobase" ,r-biobase)
1011 ("r-biocgenerics" ,r-biocgenerics)
1012 ("r-lattice" ,r-lattice)
1013 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1014 (home-page "https://bioconductor.org/packages/geneplotter")
1015 (synopsis "Graphics functions for genomic data")
1017 "This package provides functions for plotting genomic data.")
1018 (license license:artistic2.0)))
1020 (define-public r-qvalue
1027 (uri (bioconductor-uri "qvalue" version))
1030 "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5"))))
1031 (build-system r-build-system)
1033 `(("r-ggplot2" ,r-ggplot2)
1034 ("r-reshape2" ,r-reshape2)))
1035 (home-page "http://github.com/jdstorey/qvalue")
1036 (synopsis "Q-value estimation for false discovery rate control")
1038 "This package takes a list of p-values resulting from the simultaneous
1039 testing of many hypotheses and estimates their q-values and local @dfn{false
1040 discovery rate} (FDR) values. The q-value of a test measures the proportion
1041 of false positives incurred when that particular test is called significant.
1042 The local FDR measures the posterior probability the null hypothesis is true
1043 given the test's p-value. Various plots are automatically generated, allowing
1044 one to make sensible significance cut-offs. The software can be applied to
1045 problems in genomics, brain imaging, astrophysics, and data mining.")
1046 ;; Any version of the LGPL.
1047 (license license:lgpl3+)))
1049 (define-public r-diffbind
1056 (uri (bioconductor-uri "DiffBind" version))
1059 "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich"))))
1060 (properties `((upstream-name . "DiffBind")))
1061 (build-system r-build-system)
1065 `(("r-amap" ,r-amap)
1066 ("r-biocparallel" ,r-biocparallel)
1067 ("r-deseq2" ,r-deseq2)
1068 ("r-dplyr" ,r-dplyr)
1069 ("r-edger" ,r-edger)
1070 ("r-genomicalignments" ,r-genomicalignments)
1071 ("r-genomicranges" ,r-genomicranges)
1072 ("r-ggplot2" ,r-ggplot2)
1073 ("r-ggrepel" ,r-ggrepel)
1074 ("r-gplots" ,r-gplots)
1075 ("r-iranges" ,r-iranges)
1076 ("r-lattice" ,r-lattice)
1077 ("r-limma" ,r-limma)
1078 ("r-locfit" ,r-locfit)
1079 ("r-rcolorbrewer" , r-rcolorbrewer)
1081 ("r-rhtslib" ,r-rhtslib)
1082 ("r-rsamtools" ,r-rsamtools)
1083 ("r-s4vectors" ,r-s4vectors)
1084 ("r-summarizedexperiment" ,r-summarizedexperiment)
1085 ("r-systempiper" ,r-systempiper)))
1086 (home-page "http://bioconductor.org/packages/DiffBind")
1087 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1089 "This package computes differentially bound sites from multiple
1090 ChIP-seq experiments using affinity (quantitative) data. Also enables
1091 occupancy (overlap) analysis and plotting functions.")
1092 (license license:artistic2.0)))
1094 (define-public r-ripseeker
1096 (name "r-ripseeker")
1101 (uri (bioconductor-uri "RIPSeeker" version))
1104 "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43"))))
1105 (properties `((upstream-name . "RIPSeeker")))
1106 (build-system r-build-system)
1108 `(("r-s4vectors" ,r-s4vectors)
1109 ("r-iranges" ,r-iranges)
1110 ("r-genomicranges" ,r-genomicranges)
1111 ("r-summarizedexperiment" ,r-summarizedexperiment)
1112 ("r-rsamtools" ,r-rsamtools)
1113 ("r-genomicalignments" ,r-genomicalignments)
1114 ("r-rtracklayer" ,r-rtracklayer)))
1115 (home-page "http://bioconductor.org/packages/RIPSeeker")
1117 "Identifying protein-associated transcripts from RIP-seq experiments")
1119 "This package infers and discriminates RIP peaks from RIP-seq alignments
1120 using two-state HMM with negative binomial emission probability. While
1121 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1122 a suite of bioinformatics tools integrated within this self-contained software
1123 package comprehensively addressing issues ranging from post-alignments
1124 processing to visualization and annotation.")
1125 (license license:gpl2)))
1127 (define-public r-multtest
1134 (uri (bioconductor-uri "multtest" version))
1137 "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv"))))
1138 (build-system r-build-system)
1140 `(("r-survival" ,r-survival)
1141 ("r-biocgenerics" ,r-biocgenerics)
1142 ("r-biobase" ,r-biobase)
1143 ("r-mass" ,r-mass)))
1144 (home-page "http://bioconductor.org/packages/multtest")
1145 (synopsis "Resampling-based multiple hypothesis testing")
1147 "This package can do non-parametric bootstrap and permutation
1148 resampling-based multiple testing procedures (including empirical Bayes
1149 methods) for controlling the family-wise error rate (FWER), generalized
1150 family-wise error rate (gFWER), tail probability of the proportion of
1151 false positives (TPPFP), and false discovery rate (FDR). Several choices
1152 of bootstrap-based null distribution are implemented (centered, centered
1153 and scaled, quantile-transformed). Single-step and step-wise methods are
1154 available. Tests based on a variety of T- and F-statistics (including
1155 T-statistics based on regression parameters from linear and survival models
1156 as well as those based on correlation parameters) are included. When probing
1157 hypotheses with T-statistics, users may also select a potentially faster null
1158 distribution which is multivariate normal with mean zero and variance
1159 covariance matrix derived from the vector influence function. Results are
1160 reported in terms of adjusted P-values, confidence regions and test statistic
1161 cutoffs. The procedures are directly applicable to identifying differentially
1162 expressed genes in DNA microarray experiments.")
1163 (license license:lgpl3)))
1165 (define-public r-graph
1171 (uri (bioconductor-uri "graph" version))
1174 "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w"))))
1175 (build-system r-build-system)
1177 `(("r-biocgenerics" ,r-biocgenerics)))
1178 (home-page "https://bioconductor.org/packages/graph")
1179 (synopsis "Handle graph data structures in R")
1181 "This package implements some simple graph handling capabilities for R.")
1182 (license license:artistic2.0)))
1184 (define-public r-codedepends
1186 (name "r-codedepends")
1191 (uri (cran-uri "CodeDepends" version))
1194 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1195 (properties `((upstream-name . "CodeDepends")))
1196 (build-system r-build-system)
1198 `(("r-codetools" ,r-codetools)
1199 ("r-graph" ,r-graph)
1201 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1202 (synopsis "Analysis of R code for reproducible research and code comprehension")
1204 "This package provides tools for analyzing R expressions or blocks of
1205 code and determining the dependencies between them. It focuses on R scripts,
1206 but can be used on the bodies of functions. There are many facilities
1207 including the ability to summarize or get a high-level view of code,
1208 determining dependencies between variables, code improvement suggestions.")
1209 ;; Any version of the GPL
1210 (license (list license:gpl2+ license:gpl3+))))
1212 (define-public r-chippeakanno
1214 (name "r-chippeakanno")
1219 (uri (bioconductor-uri "ChIPpeakAnno" version))
1222 "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779"))))
1223 (properties `((upstream-name . "ChIPpeakAnno")))
1224 (build-system r-build-system)
1226 `(("r-annotationdbi" ,r-annotationdbi)
1227 ("r-biobase" ,r-biobase)
1228 ("r-biocgenerics" ,r-biocgenerics)
1229 ("r-biocmanager" ,r-biocmanager)
1230 ("r-biomart" ,r-biomart)
1231 ("r-biostrings" ,r-biostrings)
1232 ("r-bsgenome" ,r-bsgenome)
1234 ("r-delayedarray" ,r-delayedarray)
1235 ("r-ensembldb" ,r-ensembldb)
1236 ("r-genomeinfodb" ,r-genomeinfodb)
1237 ("r-genomicalignments" ,r-genomicalignments)
1238 ("r-genomicfeatures" ,r-genomicfeatures)
1239 ("r-genomicranges" ,r-genomicranges)
1240 ("r-go-db" ,r-go-db)
1241 ("r-graph" ,r-graph)
1243 ("r-iranges" ,r-iranges)
1244 ("r-limma" ,r-limma)
1245 ("r-matrixstats" ,r-matrixstats)
1246 ("r-multtest" ,r-multtest)
1248 ("r-regioner" ,r-regioner)
1249 ("r-rsamtools" ,r-rsamtools)
1250 ("r-rtracklayer" ,r-rtracklayer)
1251 ("r-s4vectors" ,r-s4vectors)
1252 ("r-seqinr" ,r-seqinr)
1253 ("r-summarizedexperiment" ,r-summarizedexperiment)
1254 ("r-venndiagram" ,r-venndiagram)))
1255 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1256 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1258 "The package includes functions to retrieve the sequences around the peak,
1259 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1260 custom features such as most conserved elements and other transcription factor
1261 binding sites supplied by users. Starting 2.0.5, new functions have been added
1262 for finding the peaks with bi-directional promoters with summary statistics
1263 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1264 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1265 enrichedGO (addGeneIDs).")
1266 (license license:gpl2+)))
1268 (define-public r-marray
1274 (uri (bioconductor-uri "marray" version))
1276 (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz"))))
1277 (build-system r-build-system)
1279 `(("r-limma" ,r-limma)))
1280 (home-page "http://bioconductor.org/packages/marray")
1281 (synopsis "Exploratory analysis for two-color spotted microarray data")
1282 (description "This package contains class definitions for two-color spotted
1283 microarray data. It also includes functions for data input, diagnostic plots,
1284 normalization and quality checking.")
1285 (license license:lgpl2.0+)))
1287 (define-public r-cghbase
1293 (uri (bioconductor-uri "CGHbase" version))
1295 (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm"))))
1296 (properties `((upstream-name . "CGHbase")))
1297 (build-system r-build-system)
1299 `(("r-biobase" ,r-biobase)
1300 ("r-marray" ,r-marray)))
1301 (home-page "http://bioconductor.org/packages/CGHbase")
1302 (synopsis "Base functions and classes for arrayCGH data analysis")
1303 (description "This package contains functions and classes that are needed by
1304 the @code{arrayCGH} packages.")
1305 (license license:gpl2+)))
1307 (define-public r-cghcall
1313 (uri (bioconductor-uri "CGHcall" version))
1315 (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93"))))
1316 (properties `((upstream-name . "CGHcall")))
1317 (build-system r-build-system)
1319 `(("r-biobase" ,r-biobase)
1320 ("r-cghbase" ,r-cghbase)
1321 ("r-impute" ,r-impute)
1322 ("r-dnacopy" ,r-dnacopy)
1323 ("r-snowfall" ,r-snowfall)))
1324 (home-page "http://bioconductor.org/packages/CGHcall")
1325 (synopsis "Base functions and classes for arrayCGH data analysis")
1326 (description "This package contains functions and classes that are needed by
1327 @code{arrayCGH} packages.")
1328 (license license:gpl2+)))
1330 (define-public r-qdnaseq
1336 (uri (bioconductor-uri "QDNAseq" version))
1338 (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz"))))
1339 (properties `((upstream-name . "QDNAseq")))
1340 (build-system r-build-system)
1342 `(("r-biobase" ,r-biobase)
1343 ("r-biocparallel" ,r-biocparallel)
1344 ("r-cghbase" ,r-cghbase)
1345 ("r-cghcall" ,r-cghcall)
1346 ("r-dnacopy" ,r-dnacopy)
1347 ("r-genomicranges" ,r-genomicranges)
1348 ("r-iranges" ,r-iranges)
1349 ("r-matrixstats" ,r-matrixstats)
1350 ("r-r-utils" ,r-r-utils)
1351 ("r-rsamtools" ,r-rsamtools)))
1352 (home-page "http://bioconductor.org/packages/QDNAseq")
1353 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1354 (description "The genome is divided into non-overlapping fixed-sized bins,
1355 number of sequence reads in each counted, adjusted with a simultaneous
1356 two-dimensional loess correction for sequence mappability and GC content, and
1357 filtered to remove spurious regions in the genome. Downstream steps of
1358 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1360 (license license:gpl2+)))
1362 (define-public r-bayseq
1369 (uri (bioconductor-uri "baySeq" version))
1372 "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w"))))
1373 (properties `((upstream-name . "baySeq")))
1374 (build-system r-build-system)
1376 `(("r-abind" ,r-abind)
1377 ("r-edger" ,r-edger)
1378 ("r-genomicranges" ,r-genomicranges)))
1379 (home-page "https://bioconductor.org/packages/baySeq/")
1380 (synopsis "Bayesian analysis of differential expression patterns in count data")
1382 "This package identifies differential expression in high-throughput count
1383 data, such as that derived from next-generation sequencing machines,
1384 calculating estimated posterior likelihoods of differential expression (or
1385 more complex hypotheses) via empirical Bayesian methods.")
1386 (license license:gpl3)))
1388 (define-public r-chipcomp
1395 (uri (bioconductor-uri "ChIPComp" version))
1398 "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y"))))
1399 (properties `((upstream-name . "ChIPComp")))
1400 (build-system r-build-system)
1402 `(("r-biocgenerics" ,r-biocgenerics)
1403 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1404 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1405 ("r-genomeinfodb" ,r-genomeinfodb)
1406 ("r-genomicranges" ,r-genomicranges)
1407 ("r-iranges" ,r-iranges)
1408 ("r-limma" ,r-limma)
1409 ("r-rsamtools" ,r-rsamtools)
1410 ("r-rtracklayer" ,r-rtracklayer)
1411 ("r-s4vectors" ,r-s4vectors)))
1412 (home-page "https://bioconductor.org/packages/ChIPComp")
1413 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1415 "ChIPComp implements a statistical method for quantitative comparison of
1416 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1417 sites across multiple conditions considering matching control in ChIP-seq
1419 ;; Any version of the GPL.
1420 (license license:gpl3+)))
1422 (define-public r-riboprofiling
1424 (name "r-riboprofiling")
1429 (uri (bioconductor-uri "RiboProfiling" version))
1432 "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9"))))
1433 (properties `((upstream-name . "RiboProfiling")))
1434 (build-system r-build-system)
1436 `(("r-biocgenerics" ,r-biocgenerics)
1437 ("r-biostrings" ,r-biostrings)
1438 ("r-data-table" ,r-data-table)
1439 ("r-genomeinfodb" ,r-genomeinfodb)
1440 ("r-genomicalignments" ,r-genomicalignments)
1441 ("r-genomicfeatures" ,r-genomicfeatures)
1442 ("r-genomicranges" ,r-genomicranges)
1443 ("r-ggbio" ,r-ggbio)
1444 ("r-ggplot2" ,r-ggplot2)
1445 ("r-iranges" ,r-iranges)
1447 ("r-reshape2" ,r-reshape2)
1448 ("r-rsamtools" ,r-rsamtools)
1449 ("r-rtracklayer" ,r-rtracklayer)
1450 ("r-s4vectors" ,r-s4vectors)
1451 ("r-sqldf" ,r-sqldf)))
1452 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1453 (synopsis "Ribosome profiling data analysis")
1454 (description "Starting with a BAM file, this package provides the
1455 necessary functions for quality assessment, read start position recalibration,
1456 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1457 of count data: pairs, log fold-change, codon frequency and coverage
1458 assessment, principal component analysis on codon coverage.")
1459 (license license:gpl3)))
1461 (define-public r-riboseqr
1468 (uri (bioconductor-uri "riboSeqR" version))
1471 "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga"))))
1472 (properties `((upstream-name . "riboSeqR")))
1473 (build-system r-build-system)
1475 `(("r-abind" ,r-abind)
1476 ("r-bayseq" ,r-bayseq)
1477 ("r-genomeinfodb" ,r-genomeinfodb)
1478 ("r-genomicranges" ,r-genomicranges)
1479 ("r-iranges" ,r-iranges)
1480 ("r-rsamtools" ,r-rsamtools)
1481 ("r-seqlogo" ,r-seqlogo)))
1482 (home-page "https://bioconductor.org/packages/riboSeqR/")
1483 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1485 "This package provides plotting functions, frameshift detection and
1486 parsing of genetic sequencing data from ribosome profiling experiments.")
1487 (license license:gpl3)))
1489 (define-public r-interactionset
1491 (name "r-interactionset")
1496 (uri (bioconductor-uri "InteractionSet" version))
1499 "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6"))))
1501 `((upstream-name . "InteractionSet")))
1502 (build-system r-build-system)
1504 `(("r-biocgenerics" ,r-biocgenerics)
1505 ("r-genomeinfodb" ,r-genomeinfodb)
1506 ("r-genomicranges" ,r-genomicranges)
1507 ("r-iranges" ,r-iranges)
1508 ("r-matrix" ,r-matrix)
1510 ("r-s4vectors" ,r-s4vectors)
1511 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1512 (home-page "https://bioconductor.org/packages/InteractionSet")
1513 (synopsis "Base classes for storing genomic interaction data")
1515 "This package provides the @code{GInteractions},
1516 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1517 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1519 (license license:gpl3)))
1521 (define-public r-genomicinteractions
1523 (name "r-genomicinteractions")
1528 (uri (bioconductor-uri "GenomicInteractions" version))
1531 "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p"))))
1533 `((upstream-name . "GenomicInteractions")))
1534 (build-system r-build-system)
1536 `(("r-biobase" ,r-biobase)
1537 ("r-biocgenerics" ,r-biocgenerics)
1538 ("r-data-table" ,r-data-table)
1539 ("r-dplyr" ,r-dplyr)
1540 ("r-genomeinfodb" ,r-genomeinfodb)
1541 ("r-genomicranges" ,r-genomicranges)
1542 ("r-ggplot2" ,r-ggplot2)
1543 ("r-gridextra" ,r-gridextra)
1545 ("r-igraph" ,r-igraph)
1546 ("r-interactionset" ,r-interactionset)
1547 ("r-iranges" ,r-iranges)
1548 ("r-rsamtools" ,r-rsamtools)
1549 ("r-rtracklayer" ,r-rtracklayer)
1550 ("r-s4vectors" ,r-s4vectors)
1551 ("r-stringr" ,r-stringr)))
1552 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1553 (synopsis "R package for handling genomic interaction data")
1555 "This R package provides tools for handling genomic interaction data,
1556 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1557 information and producing various plots and statistics.")
1558 (license license:gpl3)))
1560 (define-public r-ctc
1567 (uri (bioconductor-uri "ctc" version))
1570 "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am"))))
1571 (build-system r-build-system)
1572 (propagated-inputs `(("r-amap" ,r-amap)))
1573 (home-page "https://bioconductor.org/packages/ctc/")
1574 (synopsis "Cluster and tree conversion")
1576 "This package provides tools for exporting and importing classification
1577 trees and clusters to other programs.")
1578 (license license:gpl2)))
1580 (define-public r-goseq
1587 (uri (bioconductor-uri "goseq" version))
1590 "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw"))))
1591 (build-system r-build-system)
1593 `(("r-annotationdbi" ,r-annotationdbi)
1594 ("r-biasedurn" ,r-biasedurn)
1595 ("r-biocgenerics" ,r-biocgenerics)
1596 ("r-genelendatabase" ,r-genelendatabase)
1597 ("r-go-db" ,r-go-db)
1598 ("r-mgcv" ,r-mgcv)))
1599 (home-page "https://bioconductor.org/packages/goseq/")
1600 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1602 "This package provides tools to detect Gene Ontology and/or other user
1603 defined categories which are over/under represented in RNA-seq data.")
1604 (license license:lgpl2.0+)))
1606 (define-public r-glimma
1613 (uri (bioconductor-uri "Glimma" version))
1616 "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x"))))
1617 (properties `((upstream-name . "Glimma")))
1618 (build-system r-build-system)
1620 `(("r-edger" ,r-edger)
1621 ("r-jsonlite" ,r-jsonlite)
1622 ("r-s4vectors" ,r-s4vectors)))
1623 (home-page "https://github.com/Shians/Glimma")
1624 (synopsis "Interactive HTML graphics")
1626 "This package generates interactive visualisations for analysis of
1627 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1628 HTML page. The interactions are built on top of the popular static
1629 representations of analysis results in order to provide additional
1631 (license license:lgpl3)))
1633 (define-public r-rots
1640 (uri (bioconductor-uri "ROTS" version))
1643 "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77"))))
1644 (properties `((upstream-name . "ROTS")))
1645 (build-system r-build-system)
1647 `(("r-biobase" ,r-biobase)
1648 ("r-rcpp" ,r-rcpp)))
1649 (home-page "https://bioconductor.org/packages/ROTS/")
1650 (synopsis "Reproducibility-Optimized Test Statistic")
1652 "This package provides tools for calculating the
1653 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1655 (license license:gpl2+)))
1657 (define-public r-plgem
1664 (uri (bioconductor-uri "plgem" version))
1667 "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp"))))
1668 (build-system r-build-system)
1670 `(("r-biobase" ,r-biobase)
1671 ("r-mass" ,r-mass)))
1672 (home-page "http://www.genopolis.it")
1673 (synopsis "Detect differential expression in microarray and proteomics datasets")
1675 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1676 model the variance-versus-mean dependence that exists in a variety of
1677 genome-wide datasets, including microarray and proteomics data. The use of
1678 PLGEM has been shown to improve the detection of differentially expressed
1679 genes or proteins in these datasets.")
1680 (license license:gpl2)))
1682 (define-public r-inspect
1689 (uri (bioconductor-uri "INSPEcT" version))
1692 "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
1693 (properties `((upstream-name . "INSPEcT")))
1694 (build-system r-build-system)
1696 `(("r-biobase" ,r-biobase)
1697 ("r-biocgenerics" ,r-biocgenerics)
1698 ("r-biocparallel" ,r-biocparallel)
1699 ("r-deseq2" ,r-deseq2)
1700 ("r-desolve" ,r-desolve)
1701 ("r-genomicalignments" ,r-genomicalignments)
1702 ("r-genomicfeatures" ,r-genomicfeatures)
1703 ("r-genomicranges" ,r-genomicranges)
1704 ("r-iranges" ,r-iranges)
1705 ("r-plgem" ,r-plgem)
1706 ("r-preprocesscore" ,r-preprocesscore)
1708 ("r-rootsolve" ,r-rootsolve)
1709 ("r-rsamtools" ,r-rsamtools)
1710 ("r-s4vectors" ,r-s4vectors)
1711 ("r-shiny" ,r-shiny)
1712 ("r-summarizedexperiment" ,r-summarizedexperiment)
1713 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1714 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
1715 (home-page "https://bioconductor.org/packages/INSPEcT")
1716 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1718 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1719 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1720 order to evaluate synthesis, processing and degradation rates and assess via
1721 modeling the rates that determines changes in mature mRNA levels.")
1722 (license license:gpl2)))
1724 (define-public r-dnabarcodes
1726 (name "r-dnabarcodes")
1731 (uri (bioconductor-uri "DNABarcodes" version))
1734 "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0"))))
1735 (properties `((upstream-name . "DNABarcodes")))
1736 (build-system r-build-system)
1739 ("r-matrix" ,r-matrix)
1740 ("r-rcpp" ,r-rcpp)))
1741 (home-page "https://bioconductor.org/packages/DNABarcodes")
1742 (synopsis "Create and analyze DNA barcodes")
1744 "This package offers tools to create DNA barcode sets capable of
1745 correcting insertion, deletion, and substitution errors. Existing barcodes
1746 can be analyzed regarding their minimal, maximal and average distances between
1747 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
1748 demultiplexed, i.e. assigned to their original reference barcode.")
1749 (license license:gpl2)))
1751 (define-public r-ruvseq
1758 (uri (bioconductor-uri "RUVSeq" version))
1761 "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33"))))
1762 (properties `((upstream-name . "RUVSeq")))
1763 (build-system r-build-system)
1765 `(("r-biobase" ,r-biobase)
1766 ("r-edaseq" ,r-edaseq)
1767 ("r-edger" ,r-edger)
1768 ("r-mass" ,r-mass)))
1769 (home-page "https://github.com/drisso/RUVSeq")
1770 (synopsis "Remove unwanted variation from RNA-Seq data")
1772 "This package implements methods to @dfn{remove unwanted variation} (RUV)
1773 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
1775 (license license:artistic2.0)))
1777 (define-public r-biocneighbors
1779 (name "r-biocneighbors")
1784 (uri (bioconductor-uri "BiocNeighbors" version))
1787 "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg"))))
1788 (properties `((upstream-name . "BiocNeighbors")))
1789 (build-system r-build-system)
1791 `(("r-biocgenerics" ,r-biocgenerics)
1792 ("r-biocparallel" ,r-biocparallel)
1794 ("r-rcppannoy" ,r-rcppannoy)
1795 ("r-rcpphnsw" ,r-rcpphnsw)
1796 ("r-s4vectors" ,r-s4vectors)))
1797 (home-page "https://bioconductor.org/packages/BiocNeighbors")
1798 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
1800 "This package implements exact and approximate methods for nearest
1801 neighbor detection, in a framework that allows them to be easily switched
1802 within Bioconductor packages or workflows. The exact algorithm is implemented
1803 using pre-clustering with the k-means algorithm. Functions are also provided
1804 to search for all neighbors within a given distance. Parallelization is
1805 achieved for all methods using the BiocParallel framework.")
1806 (license license:gpl3)))
1808 (define-public r-biocsingular
1810 (name "r-biocsingular")
1815 (uri (bioconductor-uri "BiocSingular" version))
1818 "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5"))))
1819 (properties `((upstream-name . "BiocSingular")))
1820 (build-system r-build-system)
1822 `(("r-beachmat" ,r-beachmat)
1823 ("r-biocgenerics" ,r-biocgenerics)
1824 ("r-biocparallel" ,r-biocparallel)
1825 ("r-delayedarray" ,r-delayedarray)
1826 ("r-irlba" ,r-irlba)
1827 ("r-matrix" ,r-matrix)
1830 ("r-s4vectors" ,r-s4vectors)))
1831 (home-page "https://github.com/LTLA/BiocSingular")
1832 (synopsis "Singular value decomposition for Bioconductor packages")
1834 "This package implements exact and approximate methods for singular value
1835 decomposition and principal components analysis, in a framework that allows
1836 them to be easily switched within Bioconductor packages or workflows. Where
1837 possible, parallelization is achieved using the BiocParallel framework.")
1838 (license license:gpl3)))
1840 (define-public r-destiny
1847 (uri (bioconductor-uri "destiny" version))
1850 "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
1851 (build-system r-build-system)
1853 `(("r-biobase" ,r-biobase)
1854 ("r-biocgenerics" ,r-biocgenerics)
1855 ("r-ggplot2" ,r-ggplot2)
1856 ("r-ggthemes" ,r-ggthemes)
1857 ("r-igraph" ,r-igraph)
1858 ("r-matrix" ,r-matrix)
1859 ("r-proxy" ,r-proxy)
1861 ("r-rcppeigen" ,r-rcppeigen)
1862 ("r-scales" ,r-scales)
1863 ("r-scatterplot3d" ,r-scatterplot3d)
1864 ("r-smoother" ,r-smoother)
1865 ("r-summarizedexperiment" ,r-summarizedexperiment)
1867 (home-page "https://bioconductor.org/packages/destiny/")
1868 (synopsis "Create and plot diffusion maps")
1869 (description "This package provides tools to create and plot diffusion
1871 ;; Any version of the GPL
1872 (license license:gpl3+)))
1874 (define-public r-savr
1881 (uri (bioconductor-uri "savR" version))
1884 "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h"))))
1885 (properties `((upstream-name . "savR")))
1886 (build-system r-build-system)
1888 `(("r-ggplot2" ,r-ggplot2)
1889 ("r-gridextra" ,r-gridextra)
1890 ("r-reshape2" ,r-reshape2)
1891 ("r-scales" ,r-scales)
1893 (home-page "https://github.com/bcalder/savR")
1894 (synopsis "Parse and analyze Illumina SAV files")
1896 "This package provides tools to parse Illumina Sequence Analysis
1897 Viewer (SAV) files, access data, and generate QC plots.")
1898 (license license:agpl3+)))
1900 (define-public r-chipexoqual
1902 (name "r-chipexoqual")
1907 (uri (bioconductor-uri "ChIPexoQual" version))
1910 "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj"))))
1911 (properties `((upstream-name . "ChIPexoQual")))
1912 (build-system r-build-system)
1914 `(("r-biocparallel" ,r-biocparallel)
1915 ("r-biovizbase" ,r-biovizbase)
1916 ("r-broom" ,r-broom)
1917 ("r-data-table" ,r-data-table)
1918 ("r-dplyr" ,r-dplyr)
1919 ("r-genomeinfodb" ,r-genomeinfodb)
1920 ("r-genomicalignments" ,r-genomicalignments)
1921 ("r-genomicranges" ,r-genomicranges)
1922 ("r-ggplot2" ,r-ggplot2)
1923 ("r-hexbin" ,r-hexbin)
1924 ("r-iranges" ,r-iranges)
1925 ("r-rcolorbrewer" ,r-rcolorbrewer)
1926 ("r-rmarkdown" ,r-rmarkdown)
1927 ("r-rsamtools" ,r-rsamtools)
1928 ("r-s4vectors" ,r-s4vectors)
1929 ("r-scales" ,r-scales)
1930 ("r-viridis" ,r-viridis)))
1931 (home-page "https://github.com/keleslab/ChIPexoQual")
1932 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
1934 "This package provides a quality control pipeline for ChIP-exo/nexus
1936 (license license:gpl2+)))
1938 (define-public r-copynumber
1940 (name "r-copynumber")
1944 (uri (bioconductor-uri "copynumber" version))
1947 "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp"))))
1948 (build-system r-build-system)
1950 `(("r-s4vectors" ,r-s4vectors)
1951 ("r-iranges" ,r-iranges)
1952 ("r-genomicranges" ,r-genomicranges)
1953 ("r-biocgenerics" ,r-biocgenerics)))
1954 (home-page "https://bioconductor.org/packages/copynumber")
1955 (synopsis "Segmentation of single- and multi-track copy number data")
1957 "This package segments single- and multi-track copy number data by a
1958 penalized least squares regression method.")
1959 (license license:artistic2.0)))
1961 (define-public r-dnacopy
1968 (uri (bioconductor-uri "DNAcopy" version))
1971 "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa"))))
1972 (properties `((upstream-name . "DNAcopy")))
1973 (build-system r-build-system)
1974 (native-inputs `(("gfortran" ,gfortran)))
1975 (home-page "https://bioconductor.org/packages/DNAcopy")
1976 (synopsis "DNA copy number data analysis")
1978 "This package implements the @dfn{circular binary segmentation} (CBS)
1979 algorithm to segment DNA copy number data and identify genomic regions with
1980 abnormal copy number.")
1981 (license license:gpl2+)))
1983 ;; This is a CRAN package, but it uncharacteristically depends on a
1984 ;; Bioconductor package.
1985 (define-public r-htscluster
1987 (name "r-htscluster")
1992 (uri (cran-uri "HTSCluster" version))
1995 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
1996 (properties `((upstream-name . "HTSCluster")))
1997 (build-system r-build-system)
1999 `(("r-capushe" ,r-capushe)
2000 ("r-edger" ,r-edger)
2001 ("r-plotrix" ,r-plotrix)))
2002 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2003 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2005 "This package provides a Poisson mixture model is implemented to cluster
2006 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2007 estimation is performed using either the EM or CEM algorithm, and the slope
2008 heuristics are used for model selection (i.e., to choose the number of
2010 (license license:gpl3+)))
2012 (define-public r-deds
2019 (uri (bioconductor-uri "DEDS" version))
2022 "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs"))))
2023 (properties `((upstream-name . "DEDS")))
2024 (build-system r-build-system)
2025 (home-page "https://bioconductor.org/packages/DEDS/")
2026 (synopsis "Differential expression via distance summary for microarray data")
2028 "This library contains functions that calculate various statistics of
2029 differential expression for microarray data, including t statistics, fold
2030 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2031 also implements a new methodology called DEDS (Differential Expression via
2032 Distance Summary), which selects differentially expressed genes by integrating
2033 and summarizing a set of statistics using a weighted distance approach.")
2034 ;; Any version of the LGPL.
2035 (license license:lgpl3+)))
2037 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2039 (define-public r-nbpseq
2046 (uri (cran-uri "NBPSeq" version))
2049 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2050 (properties `((upstream-name . "NBPSeq")))
2051 (build-system r-build-system)
2053 `(("r-qvalue" ,r-qvalue)))
2054 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2055 (synopsis "Negative binomial models for RNA-Seq data")
2057 "This package provides negative binomial models for two-group comparisons
2058 and regression inferences from RNA-sequencing data.")
2059 (license license:gpl2)))
2061 (define-public r-ebseq
2068 (uri (bioconductor-uri "EBSeq" version))
2071 "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83"))))
2072 (properties `((upstream-name . "EBSeq")))
2073 (build-system r-build-system)
2075 `(("r-blockmodeling" ,r-blockmodeling)
2076 ("r-gplots" ,r-gplots)
2077 ("r-testthat" ,r-testthat)))
2078 (home-page "https://bioconductor.org/packages/EBSeq")
2079 (synopsis "Differential expression analysis of RNA-seq data")
2081 "This package provides tools for differential expression analysis at both
2082 gene and isoform level using RNA-seq data")
2083 (license license:artistic2.0)))
2085 (define-public r-lpsymphony
2087 (name "r-lpsymphony")
2092 (uri (bioconductor-uri "lpsymphony" version))
2095 "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv"))))
2096 (build-system r-build-system)
2098 `(("gfortran" ,gfortran)
2101 `(("pkg-config" ,pkg-config)))
2102 (home-page "http://r-forge.r-project.org/projects/rsymphony")
2103 (synopsis "Symphony integer linear programming solver in R")
2105 "This package was derived from Rsymphony. The package provides an R
2106 interface to SYMPHONY, a linear programming solver written in C++. The main
2107 difference between this package and Rsymphony is that it includes the solver
2108 source code, while Rsymphony expects to find header and library files on the
2109 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2110 to install interface to SYMPHONY.")
2111 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2112 ;; lpsimphony is released under the same terms.
2113 (license license:epl1.0)))
2115 (define-public r-ihw
2122 (uri (bioconductor-uri "IHW" version))
2125 "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz"))))
2126 (properties `((upstream-name . "IHW")))
2127 (build-system r-build-system)
2129 `(("r-biocgenerics" ,r-biocgenerics)
2130 ("r-fdrtool" ,r-fdrtool)
2131 ("r-lpsymphony" ,r-lpsymphony)
2132 ("r-slam" ,r-slam)))
2133 (home-page "https://bioconductor.org/packages/IHW")
2134 (synopsis "Independent hypothesis weighting")
2136 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2137 procedure that increases power compared to the method of Benjamini and
2138 Hochberg by assigning data-driven weights to each hypothesis. The input to
2139 IHW is a two-column table of p-values and covariates. The covariate can be
2140 any continuous-valued or categorical variable that is thought to be
2141 informative on the statistical properties of each hypothesis test, while it is
2142 independent of the p-value under the null hypothesis.")
2143 (license license:artistic2.0)))
2145 (define-public r-icobra
2152 (uri (bioconductor-uri "iCOBRA" version))
2155 "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q"))))
2156 (properties `((upstream-name . "iCOBRA")))
2157 (build-system r-build-system)
2159 `(("r-dplyr" ,r-dplyr)
2161 ("r-ggplot2" ,r-ggplot2)
2162 ("r-limma" ,r-limma)
2163 ("r-reshape2" ,r-reshape2)
2165 ("r-scales" ,r-scales)
2166 ("r-shiny" ,r-shiny)
2167 ("r-shinybs" ,r-shinybs)
2168 ("r-shinydashboard" ,r-shinydashboard)
2169 ("r-upsetr" ,r-upsetr)))
2170 (home-page "https://bioconductor.org/packages/iCOBRA")
2171 (synopsis "Comparison and visualization of ranking and assignment methods")
2173 "This package provides functions for calculation and visualization of
2174 performance metrics for evaluation of ranking and binary
2175 classification (assignment) methods. It also contains a Shiny application for
2176 interactive exploration of results.")
2177 (license license:gpl2+)))
2179 (define-public r-mast
2186 (uri (bioconductor-uri "MAST" version))
2189 "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx"))))
2190 (properties `((upstream-name . "MAST")))
2191 (build-system r-build-system)
2193 `(("r-abind" ,r-abind)
2195 ("r-biobase" ,r-biobase)
2196 ("r-biocgenerics" ,r-biocgenerics)
2197 ("r-data-table" ,r-data-table)
2198 ("r-ggplot2" ,r-ggplot2)
2200 ("r-progress" ,r-progress)
2201 ("r-reshape2" ,r-reshape2)
2202 ("r-s4vectors" ,r-s4vectors)
2203 ("r-singlecellexperiment" ,r-singlecellexperiment)
2204 ("r-stringr" ,r-stringr)
2205 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2206 (home-page "https://github.com/RGLab/MAST/")
2207 (synopsis "Model-based analysis of single cell transcriptomics")
2209 "This package provides methods and models for handling zero-inflated
2210 single cell assay data.")
2211 (license license:gpl2+)))
2213 (define-public r-monocle
2220 (uri (bioconductor-uri "monocle" version))
2223 "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z"))))
2224 (build-system r-build-system)
2226 `(("r-biobase" ,r-biobase)
2227 ("r-biocgenerics" ,r-biocgenerics)
2228 ("r-biocviews" ,r-biocviews)
2229 ("r-cluster" ,r-cluster)
2230 ("r-combinat" ,r-combinat)
2231 ("r-ddrtree" ,r-ddrtree)
2232 ("r-densityclust" ,r-densityclust)
2233 ("r-dplyr" ,r-dplyr)
2234 ("r-fastica" ,r-fastica)
2235 ("r-ggplot2" ,r-ggplot2)
2236 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2237 ("r-igraph" ,r-igraph)
2238 ("r-irlba" ,r-irlba)
2239 ("r-limma" ,r-limma)
2241 ("r-matrix" ,r-matrix)
2242 ("r-matrixstats" ,r-matrixstats)
2243 ("r-pheatmap" ,r-pheatmap)
2245 ("r-proxy" ,r-proxy)
2246 ("r-qlcmatrix" ,r-qlcmatrix)
2249 ("r-reshape2" ,r-reshape2)
2250 ("r-rtsne" ,r-rtsne)
2252 ("r-stringr" ,r-stringr)
2253 ("r-tibble" ,r-tibble)
2255 ("r-viridis" ,r-viridis)))
2256 (home-page "https://bioconductor.org/packages/monocle")
2257 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2259 "Monocle performs differential expression and time-series analysis for
2260 single-cell expression experiments. It orders individual cells according to
2261 progress through a biological process, without knowing ahead of time which
2262 genes define progress through that process. Monocle also performs
2263 differential expression analysis, clustering, visualization, and other useful
2264 tasks on single cell expression data. It is designed to work with RNA-Seq and
2265 qPCR data, but could be used with other types as well.")
2266 (license license:artistic2.0)))
2268 (define-public r-monocle3
2276 (url "https://github.com/cole-trapnell-lab/monocle3.git")
2278 (file-name (git-file-name name version))
2281 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2282 (build-system r-build-system)
2284 `(("r-biobase" ,r-biobase)
2285 ("r-biocgenerics" ,r-biocgenerics)
2286 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2287 ("r-dplyr" ,r-dplyr)
2288 ("r-ggplot2" ,r-ggplot2)
2289 ("r-ggrepel" ,r-ggrepel)
2291 ("r-htmlwidgets" ,r-htmlwidgets)
2292 ("r-igraph" ,r-igraph)
2293 ("r-irlba" ,r-irlba)
2294 ("r-limma" ,r-limma)
2295 ("r-lmtest" ,r-lmtest)
2297 ("r-matrix" ,r-matrix)
2298 ("r-matrix-utils" ,r-matrix-utils)
2299 ("r-pbapply" ,r-pbapply)
2300 ("r-pbmcapply" ,r-pbmcapply)
2301 ("r-pheatmap" ,r-pheatmap)
2302 ("r-plotly" ,r-plotly)
2304 ("r-proxy" ,r-proxy)
2306 ("r-purrr" ,r-purrr)
2309 ("r-rcppparallel" ,r-rcppparallel)
2310 ("r-reshape2" ,r-reshape2)
2311 ("r-reticulate" ,r-reticulate)
2312 ("r-rhpcblasctl" ,r-rhpcblasctl)
2313 ("r-rtsne" ,r-rtsne)
2314 ("r-shiny" ,r-shiny)
2316 ("r-spdep" ,r-spdep)
2317 ("r-speedglm" ,r-speedglm)
2318 ("r-stringr" ,r-stringr)
2319 ("r-singlecellexperiment" ,r-singlecellexperiment)
2320 ("r-tibble" ,r-tibble)
2321 ("r-tidyr" ,r-tidyr)
2323 ("r-viridis" ,r-viridis)))
2324 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2325 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2327 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2328 (license license:expat)))
2330 (define-public r-noiseq
2337 (uri (bioconductor-uri "NOISeq" version))
2340 "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
2341 (properties `((upstream-name . "NOISeq")))
2342 (build-system r-build-system)
2344 `(("r-biobase" ,r-biobase)
2345 ("r-matrix" ,r-matrix)))
2346 (home-page "https://bioconductor.org/packages/NOISeq")
2347 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2349 "This package provides tools to support the analysis of RNA-seq
2350 expression data or other similar kind of data. It provides exploratory plots
2351 to evaluate saturation, count distribution, expression per chromosome, type of
2352 detected features, features length, etc. It also supports the analysis of
2353 differential expression between two experimental conditions with no parametric
2355 (license license:artistic2.0)))
2357 (define-public r-scdd
2364 (uri (bioconductor-uri "scDD" version))
2367 "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf"))))
2368 (properties `((upstream-name . "scDD")))
2369 (build-system r-build-system)
2372 ("r-biocparallel" ,r-biocparallel)
2373 ("r-ebseq" ,r-ebseq)
2374 ("r-fields" ,r-fields)
2375 ("r-ggplot2" ,r-ggplot2)
2376 ("r-mclust" ,r-mclust)
2377 ("r-outliers" ,r-outliers)
2378 ("r-s4vectors" ,r-s4vectors)
2379 ("r-scran" ,r-scran)
2380 ("r-singlecellexperiment" ,r-singlecellexperiment)
2381 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2382 (home-page "https://github.com/kdkorthauer/scDD")
2383 (synopsis "Mixture modeling of single-cell RNA-seq data")
2385 "This package implements a method to analyze single-cell RNA-seq data
2386 utilizing flexible Dirichlet Process mixture models. Genes with differential
2387 distributions of expression are classified into several interesting patterns
2388 of differences between two conditions. The package also includes functions
2389 for simulating data with these patterns from negative binomial
2391 (license license:gpl2)))
2393 (define-public r-scone
2400 (uri (bioconductor-uri "scone" version))
2403 "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck"))))
2404 (build-system r-build-system)
2406 `(("r-aroma-light" ,r-aroma-light)
2407 ("r-biocparallel" ,r-biocparallel)
2409 ("r-class" ,r-class)
2410 ("r-cluster" ,r-cluster)
2411 ("r-compositions" ,r-compositions)
2412 ("r-diptest" ,r-diptest)
2413 ("r-edger" ,r-edger)
2415 ("r-gplots" ,r-gplots)
2416 ("r-hexbin" ,r-hexbin)
2417 ("r-limma" ,r-limma)
2418 ("r-matrixstats" ,r-matrixstats)
2419 ("r-mixtools" ,r-mixtools)
2420 ("r-rarpack" ,r-rarpack)
2421 ("r-rcolorbrewer" ,r-rcolorbrewer)
2422 ("r-rhdf5" ,r-rhdf5)
2423 ("r-ruvseq" ,r-ruvseq)
2424 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2425 (home-page "https://bioconductor.org/packages/scone")
2426 (synopsis "Single cell overview of normalized expression data")
2428 "SCONE is an R package for comparing and ranking the performance of
2429 different normalization schemes for single-cell RNA-seq and other
2430 high-throughput analyses.")
2431 (license license:artistic2.0)))
2433 (define-public r-geoquery
2440 (uri (bioconductor-uri "GEOquery" version))
2443 "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr"))))
2444 (properties `((upstream-name . "GEOquery")))
2445 (build-system r-build-system)
2447 `(("r-biobase" ,r-biobase)
2448 ("r-dplyr" ,r-dplyr)
2450 ("r-limma" ,r-limma)
2451 ("r-magrittr" ,r-magrittr)
2452 ("r-readr" ,r-readr)
2453 ("r-tidyr" ,r-tidyr)
2454 ("r-xml2" ,r-xml2)))
2455 (home-page "https://github.com/seandavi/GEOquery/")
2456 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2458 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2459 microarray data. Given the rich and varied nature of this resource, it is
2460 only natural to want to apply BioConductor tools to these data. GEOquery is
2461 the bridge between GEO and BioConductor.")
2462 (license license:gpl2)))
2464 (define-public r-illuminaio
2466 (name "r-illuminaio")
2471 (uri (bioconductor-uri "illuminaio" version))
2474 "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8"))))
2475 (build-system r-build-system)
2477 `(("r-base64" ,r-base64)))
2478 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2479 (synopsis "Parse Illumina microarray output files")
2481 "This package provides tools for parsing Illumina's microarray output
2482 files, including IDAT.")
2483 (license license:gpl2)))
2485 (define-public r-siggenes
2492 (uri (bioconductor-uri "siggenes" version))
2495 "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib"))))
2496 (build-system r-build-system)
2498 `(("r-biobase" ,r-biobase)
2499 ("r-multtest" ,r-multtest)
2500 ("r-scrime" ,r-scrime)))
2501 (home-page "https://bioconductor.org/packages/siggenes/")
2503 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2505 "This package provides tools for the identification of differentially
2506 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2507 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2508 Bayes Analyses of Microarrays} (EBAM).")
2509 (license license:lgpl2.0+)))
2511 (define-public r-bumphunter
2513 (name "r-bumphunter")
2518 (uri (bioconductor-uri "bumphunter" version))
2521 "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx"))))
2522 (build-system r-build-system)
2524 `(("r-annotationdbi" ,r-annotationdbi)
2525 ("r-biocgenerics" ,r-biocgenerics)
2526 ("r-dorng" ,r-dorng)
2527 ("r-foreach" ,r-foreach)
2528 ("r-genomeinfodb" ,r-genomeinfodb)
2529 ("r-genomicfeatures" ,r-genomicfeatures)
2530 ("r-genomicranges" ,r-genomicranges)
2531 ("r-iranges" ,r-iranges)
2532 ("r-iterators" ,r-iterators)
2533 ("r-limma" ,r-limma)
2534 ("r-locfit" ,r-locfit)
2535 ("r-matrixstats" ,r-matrixstats)
2536 ("r-s4vectors" ,r-s4vectors)))
2537 (home-page "https://github.com/ririzarr/bumphunter")
2538 (synopsis "Find bumps in genomic data")
2540 "This package provides tools for finding bumps in genomic data in order
2541 to identify differentially methylated regions in epigenetic epidemiology
2543 (license license:artistic2.0)))
2545 (define-public r-minfi
2552 (uri (bioconductor-uri "minfi" version))
2555 "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd"))))
2556 (build-system r-build-system)
2558 `(("r-beanplot" ,r-beanplot)
2559 ("r-biobase" ,r-biobase)
2560 ("r-biocgenerics" ,r-biocgenerics)
2561 ("r-biocparallel" ,r-biocparallel)
2562 ("r-biostrings" ,r-biostrings)
2563 ("r-bumphunter" ,r-bumphunter)
2564 ("r-data-table" ,r-data-table)
2565 ("r-delayedarray" ,r-delayedarray)
2566 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2567 ("r-genefilter" ,r-genefilter)
2568 ("r-genomeinfodb" ,r-genomeinfodb)
2569 ("r-genomicranges" ,r-genomicranges)
2570 ("r-geoquery" ,r-geoquery)
2571 ("r-hdf5array" ,r-hdf5array)
2572 ("r-illuminaio" ,r-illuminaio)
2573 ("r-iranges" ,r-iranges)
2574 ("r-lattice" ,r-lattice)
2575 ("r-limma" ,r-limma)
2577 ("r-mclust" ,r-mclust)
2579 ("r-nor1mix" ,r-nor1mix)
2580 ("r-preprocesscore" ,r-preprocesscore)
2581 ("r-quadprog" ,r-quadprog)
2582 ("r-rcolorbrewer" ,r-rcolorbrewer)
2583 ("r-reshape" ,r-reshape)
2584 ("r-s4vectors" ,r-s4vectors)
2585 ("r-siggenes" ,r-siggenes)
2586 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2587 (home-page "https://github.com/hansenlab/minfi")
2588 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2590 "This package provides tools to analyze and visualize Illumina Infinium
2591 methylation arrays.")
2592 (license license:artistic2.0)))
2594 (define-public r-methylumi
2596 (name "r-methylumi")
2601 (uri (bioconductor-uri "methylumi" version))
2604 "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f"))))
2605 (build-system r-build-system)
2607 `(("r-annotate" ,r-annotate)
2608 ("r-annotationdbi" ,r-annotationdbi)
2609 ("r-biobase" ,r-biobase)
2610 ("r-biocgenerics" ,r-biocgenerics)
2611 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2612 ("r-genefilter" ,r-genefilter)
2613 ("r-genomeinfodb" ,r-genomeinfodb)
2614 ("r-genomicranges" ,r-genomicranges)
2615 ("r-ggplot2" ,r-ggplot2)
2616 ("r-illuminaio" ,r-illuminaio)
2617 ("r-iranges" ,r-iranges)
2618 ("r-lattice" ,r-lattice)
2619 ("r-matrixstats" ,r-matrixstats)
2620 ("r-minfi" ,r-minfi)
2621 ("r-reshape2" ,r-reshape2)
2622 ("r-s4vectors" ,r-s4vectors)
2623 ("r-scales" ,r-scales)
2624 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2625 (home-page "https://bioconductor.org/packages/methylumi")
2626 (synopsis "Handle Illumina methylation data")
2628 "This package provides classes for holding and manipulating Illumina
2629 methylation data. Based on eSet, it can contain MIAME information, sample
2630 information, feature information, and multiple matrices of data. An
2631 \"intelligent\" import function, methylumiR can read the Illumina text files
2632 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2633 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2634 background correction, and quality control features for GoldenGate, Infinium,
2635 and Infinium HD arrays are also included.")
2636 (license license:gpl2)))
2638 (define-public r-lumi
2645 (uri (bioconductor-uri "lumi" version))
2648 "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba"))))
2649 (build-system r-build-system)
2651 `(("r-affy" ,r-affy)
2652 ("r-annotate" ,r-annotate)
2653 ("r-annotationdbi" ,r-annotationdbi)
2654 ("r-biobase" ,r-biobase)
2656 ("r-genomicfeatures" ,r-genomicfeatures)
2657 ("r-genomicranges" ,r-genomicranges)
2658 ("r-kernsmooth" ,r-kernsmooth)
2659 ("r-lattice" ,r-lattice)
2661 ("r-methylumi" ,r-methylumi)
2663 ("r-nleqslv" ,r-nleqslv)
2664 ("r-preprocesscore" ,r-preprocesscore)
2665 ("r-rsqlite" ,r-rsqlite)))
2666 (home-page "https://bioconductor.org/packages/lumi")
2667 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2669 "The lumi package provides an integrated solution for the Illumina
2670 microarray data analysis. It includes functions of Illumina
2671 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2672 variance stabilization, normalization and gene annotation at the probe level.
2673 It also includes the functions of processing Illumina methylation microarrays,
2674 especially Illumina Infinium methylation microarrays.")
2675 (license license:lgpl2.0+)))
2677 (define-public r-linnorm
2684 (uri (bioconductor-uri "Linnorm" version))
2687 "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5"))))
2688 (properties `((upstream-name . "Linnorm")))
2689 (build-system r-build-system)
2691 `(("r-amap" ,r-amap)
2692 ("r-apcluster" ,r-apcluster)
2693 ("r-ellipse" ,r-ellipse)
2694 ("r-fastcluster" ,r-fastcluster)
2696 ("r-ggdendro" ,r-ggdendro)
2697 ("r-ggplot2" ,r-ggplot2)
2698 ("r-gmodels" ,r-gmodels)
2699 ("r-igraph" ,r-igraph)
2700 ("r-limma" ,r-limma)
2702 ("r-mclust" ,r-mclust)
2704 ("r-rcpparmadillo" ,r-rcpparmadillo)
2705 ("r-rtsne" ,r-rtsne)
2706 ("r-statmod" ,r-statmod)
2707 ("r-vegan" ,r-vegan)
2709 (home-page "http://www.jjwanglab.org/Linnorm/")
2710 (synopsis "Linear model and normality based transformation method")
2712 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
2713 count data or any large scale count data. It transforms such datasets for
2714 parametric tests. In addition to the transformtion function (@code{Linnorm}),
2715 the following pipelines are implemented:
2718 @item Library size/batch effect normalization (@code{Linnorm.Norm})
2719 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
2720 clustering or hierarchical clustering (@code{Linnorm.tSNE},
2721 @code{Linnorm.PCA}, @code{Linnorm.HClust})
2722 @item Differential expression analysis or differential peak detection using
2723 limma (@code{Linnorm.limma})
2724 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
2725 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
2726 @item Stable gene selection for scRNA-seq data; for users without or who do
2727 not want to rely on spike-in genes (@code{Linnorm.SGenes})
2728 @item Data imputation (@code{Linnorm.DataImput}).
2731 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
2732 @code{RnaXSim} function is included for simulating RNA-seq data for the
2733 evaluation of DEG analysis methods.")
2734 (license license:expat)))
2736 (define-public r-ioniser
2743 (uri (bioconductor-uri "IONiseR" version))
2746 "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y"))))
2747 (properties `((upstream-name . "IONiseR")))
2748 (build-system r-build-system)
2750 `(("r-biocgenerics" ,r-biocgenerics)
2751 ("r-biocparallel" ,r-biocparallel)
2752 ("r-biostrings" ,r-biostrings)
2753 ("r-bit64" ,r-bit64)
2754 ("r-dplyr" ,r-dplyr)
2755 ("r-ggplot2" ,r-ggplot2)
2756 ("r-magrittr" ,r-magrittr)
2757 ("r-rhdf5" ,r-rhdf5)
2758 ("r-shortread" ,r-shortread)
2759 ("r-stringr" ,r-stringr)
2760 ("r-tibble" ,r-tibble)
2761 ("r-tidyr" ,r-tidyr)
2762 ("r-xvector" ,r-xvector)))
2763 (home-page "https://bioconductor.org/packages/IONiseR/")
2764 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
2766 "IONiseR provides tools for the quality assessment of Oxford Nanopore
2767 MinION data. It extracts summary statistics from a set of fast5 files and can
2768 be used either before or after base calling. In addition to standard
2769 summaries of the read-types produced, it provides a number of plots for
2770 visualising metrics relative to experiment run time or spatially over the
2771 surface of a flowcell.")
2772 (license license:expat)))
2774 ;; This is a CRAN package, but it depends on packages from Bioconductor.
2775 (define-public r-gkmsvm
2782 (uri (cran-uri "gkmSVM" version))
2785 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
2786 (properties `((upstream-name . "gkmSVM")))
2787 (build-system r-build-system)
2789 `(("r-biocgenerics" ,r-biocgenerics)
2790 ("r-biostrings" ,r-biostrings)
2791 ("r-genomeinfodb" ,r-genomeinfodb)
2792 ("r-genomicranges" ,r-genomicranges)
2793 ("r-iranges" ,r-iranges)
2794 ("r-kernlab" ,r-kernlab)
2797 ("r-rtracklayer" ,r-rtracklayer)
2798 ("r-s4vectors" ,r-s4vectors)
2799 ("r-seqinr" ,r-seqinr)))
2800 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
2801 (synopsis "Gapped-kmer support vector machine")
2803 "This R package provides tools for training gapped-kmer SVM classifiers
2804 for DNA and protein sequences. This package supports several sequence
2805 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
2806 (license license:gpl2+)))
2808 (define-public r-triform
2815 (uri (bioconductor-uri "triform" version))
2818 "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya"))))
2819 (build-system r-build-system)
2821 `(("r-biocgenerics" ,r-biocgenerics)
2822 ("r-iranges" ,r-iranges)
2823 ("r-yaml" ,r-yaml)))
2824 (home-page "https://bioconductor.org/packages/triform/")
2825 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
2827 "The Triform algorithm uses model-free statistics to identify peak-like
2828 distributions of TF ChIP sequencing reads, taking advantage of an improved
2829 peak definition in combination with known profile characteristics.")
2830 (license license:gpl2)))
2832 (define-public r-varianttools
2834 (name "r-varianttools")
2839 (uri (bioconductor-uri "VariantTools" version))
2842 "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql"))))
2843 (properties `((upstream-name . "VariantTools")))
2844 (build-system r-build-system)
2846 `(("r-biobase" ,r-biobase)
2847 ("r-biocgenerics" ,r-biocgenerics)
2848 ("r-biocparallel" ,r-biocparallel)
2849 ("r-biostrings" ,r-biostrings)
2850 ("r-bsgenome" ,r-bsgenome)
2851 ("r-genomeinfodb" ,r-genomeinfodb)
2852 ("r-genomicfeatures" ,r-genomicfeatures)
2853 ("r-genomicranges" ,r-genomicranges)
2854 ("r-iranges" ,r-iranges)
2855 ("r-matrix" ,r-matrix)
2856 ("r-rsamtools" ,r-rsamtools)
2857 ("r-rtracklayer" ,r-rtracklayer)
2858 ("r-s4vectors" ,r-s4vectors)
2859 ("r-variantannotation" ,r-variantannotation)))
2860 (home-page "https://bioconductor.org/packages/VariantTools/")
2861 (synopsis "Tools for exploratory analysis of variant calls")
2863 "Explore, diagnose, and compare variant calls using filters. The
2864 VariantTools package supports a workflow for loading data, calling single
2865 sample variants and tumor-specific somatic mutations or other sample-specific
2866 variant types (e.g., RNA editing). Most of the functions operate on
2867 alignments (BAM files) or datasets of called variants. The user is expected
2868 to have already aligned the reads with a separate tool, e.g., GSNAP via
2870 (license license:artistic2.0)))
2872 (define-public r-heatplus
2879 (uri (bioconductor-uri "Heatplus" version))
2882 "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6"))))
2883 (properties `((upstream-name . "Heatplus")))
2884 (build-system r-build-system)
2886 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
2887 (home-page "https://github.com/alexploner/Heatplus")
2888 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
2890 "This package provides tools to display a rectangular heatmap (intensity
2891 plot) of a data matrix. By default, both samples (columns) and features (row)
2892 of the matrix are sorted according to a hierarchical clustering, and the
2893 corresponding dendrogram is plotted. Optionally, panels with additional
2894 information about samples and features can be added to the plot.")
2895 (license license:gpl2+)))
2897 (define-public r-gosemsim
2904 (uri (bioconductor-uri "GOSemSim" version))
2907 "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg"))))
2908 (properties `((upstream-name . "GOSemSim")))
2909 (build-system r-build-system)
2911 `(("r-annotationdbi" ,r-annotationdbi)
2912 ("r-go-db" ,r-go-db)
2913 ("r-rcpp" ,r-rcpp)))
2914 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
2915 (synopsis "GO-terms semantic similarity measures")
2917 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
2918 quantitative ways to compute similarities between genes and gene groups, and
2919 have became important basis for many bioinformatics analysis approaches.
2920 GOSemSim is an R package for semantic similarity computation among GO terms,
2921 sets of GO terms, gene products and gene clusters.")
2922 (license license:artistic2.0)))
2924 (define-public r-anota
2931 (uri (bioconductor-uri "anota" version))
2934 "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c"))))
2935 (build-system r-build-system)
2937 `(("r-multtest" ,r-multtest)
2938 ("r-qvalue" ,r-qvalue)))
2939 (home-page "https://bioconductor.org/packages/anota/")
2940 (synopsis "Analysis of translational activity")
2942 "Genome wide studies of translational control is emerging as a tool to
2943 study various biological conditions. The output from such analysis is both
2944 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
2945 involved in translation (the actively translating mRNA level) for each mRNA.
2946 The standard analysis of such data strives towards identifying differential
2947 translational between two or more sample classes - i.e. differences in
2948 actively translated mRNA levels that are independent of underlying differences
2949 in cytosolic mRNA levels. This package allows for such analysis using partial
2950 variances and the random variance model. As 10s of thousands of mRNAs are
2951 analyzed in parallel the library performs a number of tests to assure that
2952 the data set is suitable for such analysis.")
2953 (license license:gpl3)))
2955 (define-public r-sigpathway
2957 (name "r-sigpathway")
2962 (uri (bioconductor-uri "sigPathway" version))
2965 "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7"))))
2966 (properties `((upstream-name . "sigPathway")))
2967 (build-system r-build-system)
2968 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
2969 (synopsis "Pathway analysis")
2971 "This package is used to conduct pathway analysis by calculating the NT_k
2972 and NE_k statistics in a statistical framework for determining whether a
2973 specified group of genes for a pathway has a coordinated association with a
2974 phenotype of interest.")
2975 (license license:gpl2)))
2977 (define-public r-fgsea
2984 (uri (bioconductor-uri "fgsea" version))
2987 "07mvv1i690q80fm8sxgdqxchamn76409vn91ppgcck2xpi6b8q6c"))))
2988 (build-system r-build-system)
2991 ("r-biocparallel" ,r-biocparallel)
2992 ("r-data-table" ,r-data-table)
2993 ("r-fastmatch" ,r-fastmatch)
2994 ("r-ggplot2" ,r-ggplot2)
2995 ("r-gridextra" ,r-gridextra)
2996 ("r-matrix" ,r-matrix)
2997 ("r-rcpp" ,r-rcpp)))
2998 (home-page "https://github.com/ctlab/fgsea/")
2999 (synopsis "Fast gene set enrichment analysis")
3001 "The package implements an algorithm for fast gene set enrichment
3002 analysis. Using the fast algorithm allows to make more permutations and get
3003 more fine grained p-values, which allows to use accurate stantard approaches
3004 to multiple hypothesis correction.")
3005 (license license:expat)))
3007 (define-public r-dose
3014 (uri (bioconductor-uri "DOSE" version))
3017 "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj"))))
3018 (properties `((upstream-name . "DOSE")))
3019 (build-system r-build-system)
3021 `(("r-annotationdbi" ,r-annotationdbi)
3022 ("r-biocparallel" ,r-biocparallel)
3023 ("r-do-db" ,r-do-db)
3024 ("r-fgsea" ,r-fgsea)
3025 ("r-ggplot2" ,r-ggplot2)
3026 ("r-gosemsim" ,r-gosemsim)
3027 ("r-qvalue" ,r-qvalue)
3028 ("r-reshape2" ,r-reshape2)
3029 ("r-s4vectors" ,r-s4vectors)))
3030 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3031 (synopsis "Disease ontology semantic and enrichment analysis")
3033 "This package implements five methods proposed by Resnik, Schlicker,
3034 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3035 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3036 including hypergeometric model and gene set enrichment analysis are also
3037 implemented for discovering disease associations of high-throughput biological
3039 (license license:artistic2.0)))
3041 (define-public r-enrichplot
3043 (name "r-enrichplot")
3048 (uri (bioconductor-uri "enrichplot" version))
3051 "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h"))))
3052 (build-system r-build-system)
3054 `(("r-annotationdbi" ,r-annotationdbi)
3055 ("r-cowplot" ,r-cowplot)
3057 ("r-europepmc" ,r-europepmc)
3058 ("r-ggplot2" ,r-ggplot2)
3059 ("r-ggplotify" ,r-ggplotify)
3060 ("r-ggraph" ,r-ggraph)
3061 ("r-ggridges" ,r-ggridges)
3062 ("r-gosemsim" ,r-gosemsim)
3063 ("r-gridextra" ,r-gridextra)
3064 ("r-igraph" ,r-igraph)
3065 ("r-purrr" ,r-purrr)
3066 ("r-rcolorbrewer" ,r-rcolorbrewer)
3067 ("r-reshape2" ,r-reshape2)
3068 ("r-upsetr" ,r-upsetr)))
3069 (home-page "https://github.com/GuangchuangYu/enrichplot")
3070 (synopsis "Visualization of functional enrichment result")
3072 "The enrichplot package implements several visualization methods for
3073 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3074 All the visualization methods are developed based on ggplot2 graphics.")
3075 (license license:artistic2.0)))
3077 (define-public r-clusterprofiler
3079 (name "r-clusterprofiler")
3084 (uri (bioconductor-uri "clusterProfiler" version))
3087 "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq"))))
3089 `((upstream-name . "clusterProfiler")))
3090 (build-system r-build-system)
3092 `(("r-annotationdbi" ,r-annotationdbi)
3094 ("r-enrichplot" ,r-enrichplot)
3095 ("r-ggplot2" ,r-ggplot2)
3096 ("r-go-db" ,r-go-db)
3097 ("r-gosemsim" ,r-gosemsim)
3098 ("r-magrittr" ,r-magrittr)
3100 ("r-qvalue" ,r-qvalue)
3101 ("r-rvcheck" ,r-rvcheck)
3102 ("r-tidyr" ,r-tidyr)))
3103 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3104 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3106 "This package implements methods to analyze and visualize functional
3107 profiles (GO and KEGG) of gene and gene clusters.")
3108 (license license:artistic2.0)))
3110 (define-public r-mlinterfaces
3112 (name "r-mlinterfaces")
3117 (uri (bioconductor-uri "MLInterfaces" version))
3120 "0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j"))))
3121 (properties `((upstream-name . "MLInterfaces")))
3122 (build-system r-build-system)
3124 `(("r-annotate" ,r-annotate)
3125 ("r-biobase" ,r-biobase)
3126 ("r-biocgenerics" ,r-biocgenerics)
3127 ("r-cluster" ,r-cluster)
3130 ("r-gdata" ,r-gdata)
3131 ("r-genefilter" ,r-genefilter)
3132 ("r-ggvis" ,r-ggvis)
3133 ("r-hwriter" ,r-hwriter)
3135 ("r-mlbench" ,r-mlbench)
3137 ("r-rcolorbrewer" ,r-rcolorbrewer)
3139 ("r-rpart" ,r-rpart)
3140 ("r-sfsmisc" ,r-sfsmisc)
3141 ("r-shiny" ,r-shiny)
3142 ("r-threejs" ,r-threejs)))
3143 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3144 (synopsis "Interfaces to R machine learning procedures")
3146 "This package provides uniform interfaces to machine learning code for
3147 data in R and Bioconductor containers.")
3148 ;; Any version of the LGPL.
3149 (license license:lgpl2.1+)))
3151 (define-public r-annaffy
3158 (uri (bioconductor-uri "annaffy" version))
3161 "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9"))))
3162 (build-system r-build-system)
3165 (modify-phases %standard-phases
3166 (add-after 'unpack 'remove-reference-to-non-free-data
3168 (substitute* "DESCRIPTION"
3172 `(("r-annotationdbi" ,r-annotationdbi)
3173 ("r-biobase" ,r-biobase)
3175 ("r-go-db" ,r-go-db)))
3176 (home-page "https://bioconductor.org/packages/annaffy/")
3177 (synopsis "Annotation tools for Affymetrix biological metadata")
3179 "This package provides functions for handling data from Bioconductor
3180 Affymetrix annotation data packages. It produces compact HTML and text
3181 reports including experimental data and URL links to many online databases.
3182 It allows searching of biological metadata using various criteria.")
3183 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3184 ;; the LGPL 2.1 is included.
3185 (license license:lgpl2.1+)))
3187 (define-public r-a4core
3194 (uri (bioconductor-uri "a4Core" version))
3197 "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7"))))
3198 (properties `((upstream-name . "a4Core")))
3199 (build-system r-build-system)
3201 `(("r-biobase" ,r-biobase)
3202 ("r-glmnet" ,r-glmnet)))
3203 (home-page "https://bioconductor.org/packages/a4Core")
3204 (synopsis "Automated Affymetrix array analysis core package")
3206 "This is the core package for the automated analysis of Affymetrix
3208 (license license:gpl3)))
3210 (define-public r-a4classif
3212 (name "r-a4classif")
3217 (uri (bioconductor-uri "a4Classif" version))
3220 "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0"))))
3221 (properties `((upstream-name . "a4Classif")))
3222 (build-system r-build-system)
3224 `(("r-a4core" ,r-a4core)
3225 ("r-a4preproc" ,r-a4preproc)
3226 ("r-glmnet" ,r-glmnet)
3227 ("r-mlinterfaces" ,r-mlinterfaces)
3230 ("r-varselrf" ,r-varselrf)))
3231 (home-page "https://bioconductor.org/packages/a4Classif/")
3232 (synopsis "Automated Affymetrix array analysis classification package")
3234 "This is the classification package for the automated analysis of
3235 Affymetrix arrays.")
3236 (license license:gpl3)))
3238 (define-public r-a4preproc
3240 (name "r-a4preproc")
3245 (uri (bioconductor-uri "a4Preproc" version))
3248 "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr"))))
3249 (properties `((upstream-name . "a4Preproc")))
3250 (build-system r-build-system)
3252 `(("r-annotationdbi" ,r-annotationdbi)))
3253 (home-page "https://bioconductor.org/packages/a4Preproc/")
3254 (synopsis "Automated Affymetrix array analysis preprocessing package")
3256 "This is a package for the automated analysis of Affymetrix arrays. It
3257 is used for preprocessing the arrays.")
3258 (license license:gpl3)))
3260 (define-public r-a4reporting
3262 (name "r-a4reporting")
3267 (uri (bioconductor-uri "a4Reporting" version))
3270 "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj"))))
3271 (properties `((upstream-name . "a4Reporting")))
3272 (build-system r-build-system)
3274 `(("r-annaffy" ,r-annaffy)
3275 ("r-xtable" ,r-xtable)))
3276 (home-page "https://bioconductor.org/packages/a4Reporting/")
3277 (synopsis "Automated Affymetrix array analysis reporting package")
3279 "This is a package for the automated analysis of Affymetrix arrays. It
3280 provides reporting features.")
3281 (license license:gpl3)))
3283 (define-public r-a4base
3290 (uri (bioconductor-uri "a4Base" version))
3293 "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1"))))
3294 (properties `((upstream-name . "a4Base")))
3295 (build-system r-build-system)
3297 `(("r-a4core" ,r-a4core)
3298 ("r-a4preproc" ,r-a4preproc)
3299 ("r-annaffy" ,r-annaffy)
3300 ("r-annotationdbi" ,r-annotationdbi)
3301 ("r-biobase" ,r-biobase)
3302 ("r-genefilter" ,r-genefilter)
3303 ("r-glmnet" ,r-glmnet)
3304 ("r-gplots" ,r-gplots)
3305 ("r-limma" ,r-limma)
3307 ("r-multtest" ,r-multtest)))
3308 (home-page "https://bioconductor.org/packages/a4Base/")
3309 (synopsis "Automated Affymetrix array analysis base package")
3311 "This package provides basic features for the automated analysis of
3312 Affymetrix arrays.")
3313 (license license:gpl3)))
3322 (uri (bioconductor-uri "a4" version))
3325 "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy"))))
3326 (build-system r-build-system)
3328 `(("r-a4base" ,r-a4base)
3329 ("r-a4classif" ,r-a4classif)
3330 ("r-a4core" ,r-a4core)
3331 ("r-a4preproc" ,r-a4preproc)
3332 ("r-a4reporting" ,r-a4reporting)))
3333 (home-page "https://bioconductor.org/packages/a4/")
3334 (synopsis "Automated Affymetrix array analysis umbrella package")
3336 "This package provides a software suite for the automated analysis of
3337 Affymetrix arrays.")
3338 (license license:gpl3)))
3340 (define-public r-abseqr
3347 (uri (bioconductor-uri "abseqR" version))
3350 "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r"))))
3351 (properties `((upstream-name . "abseqR")))
3352 (build-system r-build-system)
3354 `(("pandoc" ,ghc-pandoc)))
3356 `(("r-biocparallel" ,r-biocparallel)
3357 ("r-biocstyle" ,r-biocstyle)
3358 ("r-circlize" ,r-circlize)
3359 ("r-flexdashboard" ,r-flexdashboard)
3360 ("r-ggcorrplot" ,r-ggcorrplot)
3361 ("r-ggdendro" ,r-ggdendro)
3362 ("r-ggplot2" ,r-ggplot2)
3363 ("r-gridextra" ,r-gridextra)
3364 ("r-knitr" ,r-knitr)
3365 ("r-plotly" ,r-plotly)
3368 ("r-rcolorbrewer" ,r-rcolorbrewer)
3369 ("r-reshape2" ,r-reshape2)
3370 ("r-rmarkdown" ,r-rmarkdown)
3371 ("r-stringr" ,r-stringr)
3372 ("r-vegan" ,r-vegan)
3373 ("r-venndiagram" ,r-venndiagram)))
3374 (home-page "https://github.com/malhamdoosh/abseqR")
3375 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3377 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3378 sequencing datasets generated from antibody libraries and abseqR is one of its
3379 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3380 capabilities and allows them to generate interactive HTML reports for the
3381 convenience of viewing and sharing with other researchers. Additionally,
3382 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3383 further downstream analysis on its output.")
3384 (license license:gpl3)))
3386 (define-public r-bacon
3393 (uri (bioconductor-uri "bacon" version))
3396 "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q"))))
3397 (build-system r-build-system)
3399 `(("r-biocparallel" ,r-biocparallel)
3400 ("r-ellipse" ,r-ellipse)
3401 ("r-ggplot2" ,r-ggplot2)))
3402 (home-page "https://bioconductor.org/packages/bacon/")
3403 (synopsis "Controlling bias and inflation in association studies")
3405 "Bacon can be used to remove inflation and bias often observed in
3406 epigenome- and transcriptome-wide association studies. To this end bacon
3407 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3408 fitting a three-component normal mixture on z-scores.")
3409 (license license:gpl2+)))
3411 (define-public r-rgadem
3418 (uri (bioconductor-uri "rGADEM" version))
3421 "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18"))))
3422 (properties `((upstream-name . "rGADEM")))
3423 (build-system r-build-system)
3425 `(("r-biostrings" ,r-biostrings)
3426 ("r-bsgenome" ,r-bsgenome)
3427 ("r-iranges" ,r-iranges)
3428 ("r-seqlogo" ,r-seqlogo)))
3429 (home-page "https://bioconductor.org/packages/rGADEM/")
3430 (synopsis "De novo sequence motif discovery")
3432 "rGADEM is an efficient de novo motif discovery tool for large-scale
3433 genomic sequence data.")
3434 (license license:artistic2.0)))
3436 (define-public r-motiv
3443 (uri (bioconductor-uri "MotIV" version))
3446 "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf"))))
3447 (properties `((upstream-name . "MotIV")))
3448 (build-system r-build-system)
3452 `(("r-biocgenerics" ,r-biocgenerics)
3453 ("r-biostrings" ,r-biostrings)
3454 ("r-iranges" ,r-iranges)
3455 ("r-lattice" ,r-lattice)
3456 ("r-rgadem" ,r-rgadem)
3457 ("r-s4vectors" ,r-s4vectors)))
3458 (home-page "https://bioconductor.org/packages/MotIV/")
3459 (synopsis "Motif identification and validation")
3461 "This package is used for the identification and validation of sequence
3462 motifs. It makes use of STAMP for comparing a set of motifs to a given
3463 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3464 distributions, modules and filter motifs.")
3465 (license license:gpl2)))
3467 (define-public r-motifstack
3469 (name "r-motifstack")
3474 (uri (bioconductor-uri "motifStack" version))
3477 "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f"))))
3478 (properties `((upstream-name . "motifStack")))
3479 (build-system r-build-system)
3481 `(("r-ade4" ,r-ade4)
3482 ("r-biostrings" ,r-biostrings)
3483 ("r-grimport2" ,r-grimport2)
3484 ("r-htmlwidgets" ,r-htmlwidgets)
3485 ("r-motiv" ,r-motiv)
3486 ("r-scales" ,r-scales)
3488 (home-page "https://bioconductor.org/packages/motifStack/")
3489 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3491 "The motifStack package is designed for graphic representation of
3492 multiple motifs with different similarity scores. It works with both DNA/RNA
3493 sequence motifs and amino acid sequence motifs. In addition, it provides the
3494 flexibility for users to customize the graphic parameters such as the font
3495 type and symbol colors.")
3496 (license license:gpl2+)))
3498 (define-public r-genomicscores
3500 (name "r-genomicscores")
3505 (uri (bioconductor-uri "GenomicScores" version))
3508 "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy"))))
3509 (properties `((upstream-name . "GenomicScores")))
3510 (build-system r-build-system)
3512 `(("r-annotationhub" ,r-annotationhub)
3513 ("r-biobase" ,r-biobase)
3514 ("r-biocgenerics" ,r-biocgenerics)
3515 ("r-biostrings" ,r-biostrings)
3516 ("r-bsgenome" ,r-bsgenome)
3517 ("r-genomeinfodb" ,r-genomeinfodb)
3518 ("r-genomicranges" ,r-genomicranges)
3519 ("r-iranges" ,r-iranges)
3520 ("r-s4vectors" ,r-s4vectors)
3522 (home-page "https://github.com/rcastelo/GenomicScores/")
3523 (synopsis "Work with genome-wide position-specific scores")
3525 "This package provides infrastructure to store and access genome-wide
3526 position-specific scores within R and Bioconductor.")
3527 (license license:artistic2.0)))
3529 (define-public r-atacseqqc
3531 (name "r-atacseqqc")
3536 (uri (bioconductor-uri "ATACseqQC" version))
3539 "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
3540 (properties `((upstream-name . "ATACseqQC")))
3541 (build-system r-build-system)
3543 `(("r-biocgenerics" ,r-biocgenerics)
3544 ("r-biostrings" ,r-biostrings)
3545 ("r-bsgenome" ,r-bsgenome)
3546 ("r-chippeakanno" ,r-chippeakanno)
3547 ("r-edger" ,r-edger)
3548 ("r-genomeinfodb" ,r-genomeinfodb)
3549 ("r-genomicalignments" ,r-genomicalignments)
3550 ("r-genomicranges" ,r-genomicranges)
3551 ("r-genomicscores" ,r-genomicscores)
3552 ("r-iranges" ,r-iranges)
3553 ("r-kernsmooth" ,r-kernsmooth)
3554 ("r-limma" ,r-limma)
3555 ("r-motifstack" ,r-motifstack)
3556 ("r-preseqr" ,r-preseqr)
3557 ("r-randomforest" ,r-randomforest)
3558 ("r-rsamtools" ,r-rsamtools)
3559 ("r-rtracklayer" ,r-rtracklayer)
3560 ("r-s4vectors" ,r-s4vectors)))
3561 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3562 (synopsis "ATAC-seq quality control")
3564 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3565 sequencing, is a rapid and sensitive method for chromatin accessibility
3566 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3567 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3568 assess whether their ATAC-seq experiment is successful. It includes
3569 diagnostic plots of fragment size distribution, proportion of mitochondria
3570 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3572 (license license:gpl2+)))
3574 (define-public r-gofuncr
3581 (uri (bioconductor-uri "GOfuncR" version))
3584 "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm"))))
3585 (properties `((upstream-name . "GOfuncR")))
3586 (build-system r-build-system)
3588 `(("r-annotationdbi" ,r-annotationdbi)
3589 ("r-genomicranges" ,r-genomicranges)
3590 ("r-gtools" ,r-gtools)
3591 ("r-iranges" ,r-iranges)
3592 ("r-mapplots" ,r-mapplots)
3594 ("r-vioplot" ,r-vioplot)))
3595 (home-page "https://bioconductor.org/packages/GOfuncR/")
3596 (synopsis "Gene ontology enrichment using FUNC")
3598 "GOfuncR performs a gene ontology enrichment analysis based on the
3599 ontology enrichment software FUNC. GO-annotations are obtained from
3600 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3601 included in the package and updated regularly. GOfuncR provides the standard
3602 candidate vs background enrichment analysis using the hypergeometric test, as
3603 well as three additional tests:
3606 @item the Wilcoxon rank-sum test that is used when genes are ranked,
3607 @item a binomial test that is used when genes are associated with two counts,
3609 @item a Chi-square or Fisher's exact test that is used in cases when genes are
3610 associated with four counts.
3613 To correct for multiple testing and interdependency of the tests, family-wise
3614 error rates are computed based on random permutations of the gene-associated
3615 variables. GOfuncR also provides tools for exploring the ontology graph and
3616 the annotations, and options to take gene-length or spatial clustering of
3617 genes into account. It is also possible to provide custom gene coordinates,
3618 annotations and ontologies.")
3619 (license license:gpl2+)))
3621 (define-public r-abaenrichment
3623 (name "r-abaenrichment")
3628 (uri (bioconductor-uri "ABAEnrichment" version))
3631 "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
3632 (properties `((upstream-name . "ABAEnrichment")))
3633 (build-system r-build-system)
3635 `(("r-abadata" ,r-abadata)
3636 ("r-data-table" ,r-data-table)
3637 ("r-gofuncr" ,r-gofuncr)
3638 ("r-gplots" ,r-gplots)
3639 ("r-gtools" ,r-gtools)
3640 ("r-rcpp" ,r-rcpp)))
3641 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
3642 (synopsis "Gene expression enrichment in human brain regions")
3644 "The package ABAEnrichment is designed to test for enrichment of user
3645 defined candidate genes in the set of expressed genes in different human brain
3646 regions. The core function @code{aba_enrich} integrates the expression of the
3647 candidate gene set (averaged across donors) and the structural information of
3648 the brain using an ontology, both provided by the Allen Brain Atlas project.")
3649 (license license:gpl2+)))
3651 (define-public r-annotationfuncs
3653 (name "r-annotationfuncs")
3658 (uri (bioconductor-uri "AnnotationFuncs" version))
3661 "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3"))))
3663 `((upstream-name . "AnnotationFuncs")))
3664 (build-system r-build-system)
3666 `(("r-annotationdbi" ,r-annotationdbi)
3668 (home-page "https://www.iysik.com/r/annotationfuncs")
3669 (synopsis "Annotation translation functions")
3671 "This package provides functions for handling translating between
3672 different identifieres using the Biocore Data Team data-packages (e.g.
3673 @code{org.Bt.eg.db}).")
3674 (license license:gpl2)))
3676 (define-public r-annotationtools
3678 (name "r-annotationtools")
3683 (uri (bioconductor-uri "annotationTools" version))
3686 "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1"))))
3688 `((upstream-name . "annotationTools")))
3689 (build-system r-build-system)
3690 (propagated-inputs `(("r-biobase" ,r-biobase)))
3691 (home-page "https://bioconductor.org/packages/annotationTools/")
3692 (synopsis "Annotate microarrays and perform gene expression analyses")
3694 "This package provides functions to annotate microarrays, find orthologs,
3695 and integrate heterogeneous gene expression profiles using annotation and
3696 other molecular biology information available as flat file database (plain
3698 ;; Any version of the GPL.
3699 (license (list license:gpl2+))))
3701 (define-public r-allelicimbalance
3703 (name "r-allelicimbalance")
3708 (uri (bioconductor-uri "AllelicImbalance" version))
3711 "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng"))))
3713 `((upstream-name . "AllelicImbalance")))
3714 (build-system r-build-system)
3716 `(("r-annotationdbi" ,r-annotationdbi)
3717 ("r-biocgenerics" ,r-biocgenerics)
3718 ("r-biostrings" ,r-biostrings)
3719 ("r-bsgenome" ,r-bsgenome)
3720 ("r-genomeinfodb" ,r-genomeinfodb)
3721 ("r-genomicalignments" ,r-genomicalignments)
3722 ("r-genomicfeatures" ,r-genomicfeatures)
3723 ("r-genomicranges" ,r-genomicranges)
3724 ("r-gridextra" ,r-gridextra)
3726 ("r-iranges" ,r-iranges)
3727 ("r-lattice" ,r-lattice)
3728 ("r-latticeextra" ,r-latticeextra)
3730 ("r-rsamtools" ,r-rsamtools)
3731 ("r-s4vectors" ,r-s4vectors)
3732 ("r-seqinr" ,r-seqinr)
3733 ("r-summarizedexperiment" ,r-summarizedexperiment)
3734 ("r-variantannotation" ,r-variantannotation)))
3735 (home-page "https://github.com/pappewaio/AllelicImbalance")
3736 (synopsis "Investigate allele-specific expression")
3738 "This package provides a framework for allele-specific expression
3739 investigation using RNA-seq data.")
3740 (license license:gpl3)))
3742 (define-public r-aucell
3749 (uri (bioconductor-uri "AUCell" version))
3752 "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b"))))
3753 (properties `((upstream-name . "AUCell")))
3754 (build-system r-build-system)
3756 `(("r-data-table" ,r-data-table)
3757 ("r-gseabase" ,r-gseabase)
3758 ("r-mixtools" ,r-mixtools)
3759 ("r-r-utils" ,r-r-utils)
3760 ("r-shiny" ,r-shiny)
3761 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3762 (home-page "https://bioconductor.org/packages/AUCell/")
3763 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
3765 "AUCell allows to identify cells with active gene sets (e.g. signatures,
3766 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
3767 Under the Curve} (AUC) to calculate whether a critical subset of the input
3768 gene set is enriched within the expressed genes for each cell. The
3769 distribution of AUC scores across all the cells allows exploring the relative
3770 expression of the signature. Since the scoring method is ranking-based,
3771 AUCell is independent of the gene expression units and the normalization
3772 procedure. In addition, since the cells are evaluated individually, it can
3773 easily be applied to bigger datasets, subsetting the expression matrix if
3775 (license license:gpl3)))
3777 (define-public r-ebimage
3784 (uri (bioconductor-uri "EBImage" version))
3787 "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq"))))
3788 (properties `((upstream-name . "EBImage")))
3789 (build-system r-build-system)
3791 `(("r-abind" ,r-abind)
3792 ("r-biocgenerics" ,r-biocgenerics)
3793 ("r-fftwtools" ,r-fftwtools)
3794 ("r-htmltools" ,r-htmltools)
3795 ("r-htmlwidgets" ,r-htmlwidgets)
3797 ("r-locfit" ,r-locfit)
3799 ("r-rcurl" ,r-rcurl)
3800 ("r-tiff" ,r-tiff)))
3802 `(("r-knitr" ,r-knitr))) ; for vignettes
3803 (home-page "https://github.com/aoles/EBImage")
3804 (synopsis "Image processing and analysis toolbox for R")
3806 "EBImage provides general purpose functionality for image processing and
3807 analysis. In the context of (high-throughput) microscopy-based cellular
3808 assays, EBImage offers tools to segment cells and extract quantitative
3809 cellular descriptors. This allows the automation of such tasks using the R
3810 programming language and facilitates the use of other tools in the R
3811 environment for signal processing, statistical modeling, machine learning and
3812 visualization with image data.")
3813 ;; Any version of the LGPL.
3814 (license license:lgpl2.1+)))
3816 (define-public r-yamss
3823 (uri (bioconductor-uri "yamss" version))
3826 "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23"))))
3827 (build-system r-build-system)
3829 `(("r-biocgenerics" ,r-biocgenerics)
3830 ("r-data-table" ,r-data-table)
3831 ("r-ebimage" ,r-ebimage)
3832 ("r-iranges" ,r-iranges)
3833 ("r-limma" ,r-limma)
3834 ("r-matrix" ,r-matrix)
3836 ("r-s4vectors" ,r-s4vectors)
3837 ("r-summarizedexperiment"
3838 ,r-summarizedexperiment)))
3839 (home-page "https://github.com/hansenlab/yamss")
3840 (synopsis "Tools for high-throughput metabolomics")
3842 "This package provides tools to analyze and visualize high-throughput
3843 metabolomics data acquired using chromatography-mass spectrometry. These tools
3844 preprocess data in a way that enables reliable and powerful differential
3846 (license license:artistic2.0)))
3848 (define-public r-gtrellis
3855 (uri (bioconductor-uri "gtrellis" version))
3858 "00d5swg3brnx8ryzpg7hp3mg9hx3vz4yd1lv2chlp2pj2rhsir1y"))))
3859 (build-system r-build-system)
3861 `(("r-circlize" ,r-circlize)
3862 ("r-genomicranges" ,r-genomicranges)
3863 ("r-getoptlong" ,r-getoptlong)
3864 ("r-iranges" ,r-iranges)))
3865 (home-page "https://github.com/jokergoo/gtrellis")
3866 (synopsis "Genome level Trellis layout")
3868 "Genome level Trellis graph visualizes genomic data conditioned by
3869 genomic categories (e.g. chromosomes). For each genomic category, multiple
3870 dimensional data which are represented as tracks describe different features
3871 from different aspects. This package provides high flexibility to arrange
3872 genomic categories and to add self-defined graphics in the plot.")
3873 (license license:expat)))
3875 (define-public r-somaticsignatures
3877 (name "r-somaticsignatures")
3882 (uri (bioconductor-uri "SomaticSignatures" version))
3885 "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx"))))
3887 `((upstream-name . "SomaticSignatures")))
3888 (build-system r-build-system)
3890 `(("r-biobase" ,r-biobase)
3891 ("r-biostrings" ,r-biostrings)
3892 ("r-genomeinfodb" ,r-genomeinfodb)
3893 ("r-genomicranges" ,r-genomicranges)
3894 ("r-ggbio" ,r-ggbio)
3895 ("r-ggplot2" ,r-ggplot2)
3896 ("r-iranges" ,r-iranges)
3898 ("r-pcamethods" ,r-pcamethods)
3899 ("r-proxy" ,r-proxy)
3900 ("r-reshape2" ,r-reshape2)
3901 ("r-s4vectors" ,r-s4vectors)
3902 ("r-variantannotation" ,r-variantannotation)))
3903 (home-page "https://github.com/juliangehring/SomaticSignatures")
3904 (synopsis "Somatic signatures")
3906 "This package identifies mutational signatures of @dfn{single nucleotide
3907 variants} (SNVs). It provides a infrastructure related to the methodology
3908 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
3909 decomposition algorithms.")
3910 (license license:expat)))
3912 (define-public r-yapsa
3919 (uri (bioconductor-uri "YAPSA" version))
3922 "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q"))))
3923 (properties `((upstream-name . "YAPSA")))
3924 (build-system r-build-system)
3926 `(("r-circlize" ,r-circlize)
3927 ("r-complexheatmap" ,r-complexheatmap)
3928 ("r-corrplot" ,r-corrplot)
3929 ("r-dendextend" ,r-dendextend)
3930 ("r-genomeinfodb" ,r-genomeinfodb)
3931 ("r-genomicranges" ,r-genomicranges)
3932 ("r-getoptlong" ,r-getoptlong)
3933 ("r-ggplot2" ,r-ggplot2)
3934 ("r-gridextra" ,r-gridextra)
3935 ("r-gtrellis" ,r-gtrellis)
3936 ("r-keggrest" ,r-keggrest)
3938 ("r-pmcmr" ,r-pmcmr)
3939 ("r-reshape2" ,r-reshape2)
3940 ("r-somaticsignatures" ,r-somaticsignatures)
3941 ("r-variantannotation" ,r-variantannotation)))
3942 (home-page "https://bioconductor.org/packages/YAPSA/")
3943 (synopsis "Yet another package for signature analysis")
3945 "This package provides functions and routines useful in the analysis of
3946 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
3947 functions to perform a signature analysis with known signatures and a
3948 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
3950 (license license:gpl3)))
3952 (define-public r-gcrma
3959 (uri (bioconductor-uri "gcrma" version))
3962 "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4"))))
3963 (build-system r-build-system)
3965 `(("r-affy" ,r-affy)
3966 ("r-affyio" ,r-affyio)
3967 ("r-biobase" ,r-biobase)
3968 ("r-biocmanager" ,r-biocmanager)
3969 ("r-biostrings" ,r-biostrings)
3970 ("r-xvector" ,r-xvector)))
3971 (home-page "https://bioconductor.org/packages/gcrma/")
3972 (synopsis "Background adjustment using sequence information")
3974 "Gcrma adjusts for background intensities in Affymetrix array data which
3975 include optical noise and @dfn{non-specific binding} (NSB). The main function
3976 @code{gcrma} converts background adjusted probe intensities to expression
3977 measures using the same normalization and summarization methods as a
3978 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
3979 to estimate probe affinity to NSB. The sequence information is summarized in
3980 a more complex way than the simple GC content. Instead, the base types (A, T,
3981 G or C) at each position along the probe determine the affinity of each probe.
3982 The parameters of the position-specific base contributions to the probe
3983 affinity is estimated in an NSB experiment in which only NSB but no
3984 gene-specific bidning is expected.")
3985 ;; Any version of the LGPL
3986 (license license:lgpl2.1+)))
3988 (define-public r-simpleaffy
3990 (name "r-simpleaffy")
3995 (uri (bioconductor-uri "simpleaffy" version))
3998 "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a"))))
3999 (build-system r-build-system)
4001 `(("r-affy" ,r-affy)
4002 ("r-biobase" ,r-biobase)
4003 ("r-biocgenerics" ,r-biocgenerics)
4004 ("r-gcrma" ,r-gcrma)
4005 ("r-genefilter" ,r-genefilter)))
4006 (home-page "https://bioconductor.org/packages/simpleaffy/")
4007 (synopsis "Very simple high level analysis of Affymetrix data")
4009 "This package provides high level functions for reading Affy @file{.CEL}
4010 files, phenotypic data, and then computing simple things with it, such as
4011 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4012 library. It also has some basic scatter plot functions and mechanisms for
4013 generating high resolution journal figures.")
4014 (license license:gpl2+)))
4016 (define-public r-yaqcaffy
4023 (uri (bioconductor-uri "yaqcaffy" version))
4026 "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670"))))
4027 (build-system r-build-system)
4029 `(("r-simpleaffy" ,r-simpleaffy)))
4030 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4031 (synopsis "Affymetrix quality control and reproducibility analysis")
4033 "This is a package that can be used for quality control of Affymetrix
4034 GeneChip expression data and reproducibility analysis of human whole genome
4035 chips with the MAQC reference datasets.")
4036 (license license:artistic2.0)))
4038 (define-public r-quantro
4045 (uri (bioconductor-uri "quantro" version))
4048 "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab"))))
4049 (build-system r-build-system)
4051 `(("r-biobase" ,r-biobase)
4052 ("r-doparallel" ,r-doparallel)
4053 ("r-foreach" ,r-foreach)
4054 ("r-ggplot2" ,r-ggplot2)
4055 ("r-iterators" ,r-iterators)
4056 ("r-minfi" ,r-minfi)
4057 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4058 (home-page "https://bioconductor.org/packages/quantro/")
4059 (synopsis "Test for when to use quantile normalization")
4061 "This package provides a data-driven test for the assumptions of quantile
4062 normalization using raw data such as objects that inherit eSets (e.g.
4063 ExpressionSet, MethylSet). Group level information about each sample (such as
4064 Tumor / Normal status) must also be provided because the test assesses if
4065 there are global differences in the distributions between the user-defined
4067 (license license:gpl3+)))
4069 (define-public r-yarn
4076 (uri (bioconductor-uri "yarn" version))
4079 "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6"))))
4080 (build-system r-build-system)
4082 `(("r-biobase" ,r-biobase)
4083 ("r-biomart" ,r-biomart)
4084 ("r-downloader" ,r-downloader)
4085 ("r-edger" ,r-edger)
4086 ("r-gplots" ,r-gplots)
4087 ("r-limma" ,r-limma)
4088 ("r-matrixstats" ,r-matrixstats)
4089 ("r-preprocesscore" ,r-preprocesscore)
4090 ("r-quantro" ,r-quantro)
4091 ("r-rcolorbrewer" ,r-rcolorbrewer)
4092 ("r-readr" ,r-readr)))
4093 (home-page "https://bioconductor.org/packages/yarn/")
4094 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4096 "Expedite large RNA-Seq analyses using a combination of previously
4097 developed tools. YARN is meant to make it easier for the user in performing
4098 basic mis-annotation quality control, filtering, and condition-aware
4099 normalization. YARN leverages many Bioconductor tools and statistical
4100 techniques to account for the large heterogeneity and sparsity found in very
4101 large RNA-seq experiments.")
4102 (license license:artistic2.0)))
4104 (define-public r-roar
4111 (uri (bioconductor-uri "roar" version))
4114 "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7"))))
4115 (build-system r-build-system)
4117 `(("r-biocgenerics" ,r-biocgenerics)
4118 ("r-genomeinfodb" ,r-genomeinfodb)
4119 ("r-genomicalignments" ,r-genomicalignments)
4120 ("r-genomicranges" ,r-genomicranges)
4121 ("r-iranges" ,r-iranges)
4122 ("r-rtracklayer" ,r-rtracklayer)
4123 ("r-s4vectors" ,r-s4vectors)
4124 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4125 (home-page "https://github.com/vodkatad/roar/")
4126 (synopsis "Identify differential APA usage from RNA-seq alignments")
4128 "This package provides tools for identifying preferential usage of APA
4129 sites, comparing two biological conditions, starting from known alternative
4130 sites and alignments obtained from standard RNA-seq experiments.")
4131 (license license:gpl3)))
4133 (define-public r-xbseq
4140 (uri (bioconductor-uri "XBSeq" version))
4143 "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy"))))
4144 (properties `((upstream-name . "XBSeq")))
4145 (build-system r-build-system)
4147 `(("r-biobase" ,r-biobase)
4148 ("r-deseq2" ,r-deseq2)
4149 ("r-dplyr" ,r-dplyr)
4150 ("r-ggplot2" ,r-ggplot2)
4151 ("r-locfit" ,r-locfit)
4152 ("r-magrittr" ,r-magrittr)
4153 ("r-matrixstats" ,r-matrixstats)
4154 ("r-pracma" ,r-pracma)
4155 ("r-roar" ,r-roar)))
4156 (home-page "https://github.com/Liuy12/XBSeq")
4157 (synopsis "Test for differential expression for RNA-seq data")
4159 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4160 expression} (DE), where a statistical model was established based on the
4161 assumption that observed signals are the convolution of true expression
4162 signals and sequencing noises. The mapped reads in non-exonic regions are
4163 considered as sequencing noises, which follows a Poisson distribution. Given
4164 measurable observed signal and background noise from RNA-seq data, true
4165 expression signals, assuming governed by the negative binomial distribution,
4166 can be delineated and thus the accurate detection of differential expressed
4168 (license license:gpl3+)))
4170 (define-public r-massspecwavelet
4172 (name "r-massspecwavelet")
4177 (uri (bioconductor-uri "MassSpecWavelet" version))
4180 "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
4182 `((upstream-name . "MassSpecWavelet")))
4183 (build-system r-build-system)
4185 `(("r-waveslim" ,r-waveslim)))
4186 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4187 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4189 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4190 data mainly through the use of wavelet transforms. It supports peak detection
4191 based on @dfn{Continuous Wavelet Transform} (CWT).")
4192 (license license:lgpl2.0+)))
4194 (define-public r-xcms
4201 (uri (bioconductor-uri "xcms" version))
4204 "06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g"))))
4205 (build-system r-build-system)
4207 `(("r-biobase" ,r-biobase)
4208 ("r-biocgenerics" ,r-biocgenerics)
4209 ("r-biocparallel" ,r-biocparallel)
4210 ("r-lattice" ,r-lattice)
4211 ("r-massspecwavelet" ,r-massspecwavelet)
4212 ("r-msnbase" ,r-msnbase)
4213 ("r-multtest" ,r-multtest)
4216 ("r-protgenerics" ,r-protgenerics)
4218 ("r-rcolorbrewer" ,r-rcolorbrewer)
4219 ("r-robustbase" ,r-robustbase)
4220 ("r-s4vectors" ,r-s4vectors)))
4221 (home-page "https://bioconductor.org/packages/xcms/")
4222 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4224 "This package provides a framework for processing and visualization of
4225 chromatographically separated and single-spectra mass spectral data. It
4226 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4227 data for high-throughput, untargeted analyte profiling.")
4228 (license license:gpl2+)))
4230 (define-public r-wrench
4237 (uri (bioconductor-uri "Wrench" version))
4240 "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
4241 (properties `((upstream-name . "Wrench")))
4242 (build-system r-build-system)
4244 `(("r-limma" ,r-limma)
4245 ("r-locfit" ,r-locfit)
4246 ("r-matrixstats" ,r-matrixstats)))
4247 (home-page "https://github.com/HCBravoLab/Wrench")
4248 (synopsis "Wrench normalization for sparse count data")
4250 "Wrench is a package for normalization sparse genomic count data, like
4251 that arising from 16s metagenomic surveys.")
4252 (license license:artistic2.0)))
4254 (define-public r-wiggleplotr
4256 (name "r-wiggleplotr")
4261 (uri (bioconductor-uri "wiggleplotr" version))
4264 "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
4265 (build-system r-build-system)
4267 `(("r-assertthat" ,r-assertthat)
4268 ("r-cowplot" ,r-cowplot)
4269 ("r-dplyr" ,r-dplyr)
4270 ("r-genomeinfodb" ,r-genomeinfodb)
4271 ("r-genomicranges" ,r-genomicranges)
4272 ("r-ggplot2" ,r-ggplot2)
4273 ("r-iranges" ,r-iranges)
4274 ("r-purrr" ,r-purrr)
4275 ("r-rtracklayer" ,r-rtracklayer)
4276 ("r-s4vectors" ,r-s4vectors)))
4277 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4278 (synopsis "Make read coverage plots from BigWig files")
4280 "This package provides tools to visualize read coverage from sequencing
4281 experiments together with genomic annotations (genes, transcripts, peaks).
4282 Introns of long transcripts can be rescaled to a fixed length for better
4283 visualization of exonic read coverage.")
4284 (license license:asl2.0)))
4286 (define-public r-widgettools
4288 (name "r-widgettools")
4293 (uri (bioconductor-uri "widgetTools" version))
4296 "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
4297 (properties `((upstream-name . "widgetTools")))
4298 (build-system r-build-system)
4299 (home-page "https://bioconductor.org/packages/widgetTools/")
4300 (synopsis "Tools for creating interactive tcltk widgets")
4302 "This package contains tools to support the construction of tcltk
4304 ;; Any version of the LGPL.
4305 (license license:lgpl3+)))
4307 (define-public r-webbioc
4314 (uri (bioconductor-uri "webbioc" version))
4317 "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
4318 (build-system r-build-system)
4320 `(("netpbm" ,netpbm)
4323 `(("r-affy" ,r-affy)
4324 ("r-annaffy" ,r-annaffy)
4325 ("r-biobase" ,r-biobase)
4326 ("r-biocmanager" ,r-biocmanager)
4327 ("r-gcrma" ,r-gcrma)
4328 ("r-multtest" ,r-multtest)
4329 ("r-qvalue" ,r-qvalue)
4331 (home-page "https://www.bioconductor.org/")
4332 (synopsis "Bioconductor web interface")
4334 "This package provides an integrated web interface for doing microarray
4335 analysis using several of the Bioconductor packages. It is intended to be
4336 deployed as a centralized bioinformatics resource for use by many users.
4337 Currently only Affymetrix oligonucleotide analysis is supported.")
4338 (license license:gpl2+)))
4340 (define-public r-zfpkm
4347 (uri (bioconductor-uri "zFPKM" version))
4350 "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
4351 (properties `((upstream-name . "zFPKM")))
4352 (build-system r-build-system)
4354 `(("r-checkmate" ,r-checkmate)
4355 ("r-dplyr" ,r-dplyr)
4356 ("r-ggplot2" ,r-ggplot2)
4357 ("r-summarizedexperiment" ,r-summarizedexperiment)
4358 ("r-tidyr" ,r-tidyr)))
4359 (home-page "https://github.com/ronammar/zFPKM/")
4360 (synopsis "Functions to facilitate zFPKM transformations")
4362 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
4363 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
4365 (license license:gpl3)))
4367 (define-public r-rbowtie2
4374 (uri (bioconductor-uri "Rbowtie2" version))
4377 "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
4378 (properties `((upstream-name . "Rbowtie2")))
4379 (build-system r-build-system)
4382 (home-page "https://bioconductor.org/packages/Rbowtie2/")
4383 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
4385 "This package provides an R wrapper of the popular @code{bowtie2}
4386 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
4387 rapid adapter trimming, identification, and read merging.")
4388 (license license:gpl3+)))
4390 (define-public r-progeny
4397 (uri (bioconductor-uri "progeny" version))
4400 "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
4401 (build-system r-build-system)
4402 (propagated-inputs `(("r-biobase" ,r-biobase)))
4403 (home-page "https://github.com/saezlab/progeny")
4404 (synopsis "Pathway responsive gene activity inference")
4406 "This package provides a function to infer pathway activity from gene
4407 expression. It contains the linear model inferred in the publication
4408 \"Perturbation-response genes reveal signaling footprints in cancer gene
4410 (license license:asl2.0)))
4412 (define-public r-arrmnormalization
4414 (name "r-arrmnormalization")
4419 (uri (bioconductor-uri "ARRmNormalization" version))
4422 "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
4424 `((upstream-name . "ARRmNormalization")))
4425 (build-system r-build-system)
4426 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
4427 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
4428 (synopsis "Adaptive robust regression normalization for methylation data")
4430 "This is a package to perform the @dfn{Adaptive Robust Regression
4431 method} (ARRm) for the normalization of methylation data from the Illumina
4432 Infinium HumanMethylation 450k assay.")
4433 (license license:artistic2.0)))
4435 (define-public r-biocfilecache
4437 (name "r-biocfilecache")
4442 (uri (bioconductor-uri "BiocFileCache" version))
4445 "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb"))))
4446 (properties `((upstream-name . "BiocFileCache")))
4447 (build-system r-build-system)
4449 `(("r-curl" ,r-curl)
4451 ("r-dbplyr" ,r-dbplyr)
4452 ("r-dplyr" ,r-dplyr)
4454 ("r-rappdirs" ,r-rappdirs)
4455 ("r-rsqlite" ,r-rsqlite)))
4456 (home-page "https://bioconductor.org/packages/BiocFileCache/")
4457 (synopsis "Manage files across sessions")
4459 "This package creates a persistent on-disk cache of files that the user
4460 can add, update, and retrieve. It is useful for managing resources (such as
4461 custom Txdb objects) that are costly or difficult to create, web resources,
4462 and data files used across sessions.")
4463 (license license:artistic2.0)))
4465 (define-public r-iclusterplus
4467 (name "r-iclusterplus")
4472 (uri (bioconductor-uri "iClusterPlus" version))
4475 "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq"))))
4476 (properties `((upstream-name . "iClusterPlus")))
4477 (build-system r-build-system)
4478 (native-inputs `(("gfortran" ,gfortran)))
4479 (home-page "https://bioconductor.org/packages/iClusterPlus/")
4480 (synopsis "Integrative clustering of multi-type genomic data")
4482 "iClusterPlus is developed for integrative clustering analysis of
4483 multi-type genomic data and is an enhanced version of iCluster proposed and
4484 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
4485 from the experiments where biological samples (e.g. tumor samples) are
4486 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
4487 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
4488 on. In the iClusterPlus model, binary observations such as somatic mutation
4489 are modeled as Binomial processes; categorical observations such as copy
4490 number states are realizations of Multinomial random variables; counts are
4491 modeled as Poisson random processes; and continuous measures are modeled by
4492 Gaussian distributions.")
4493 (license license:gpl2+)))
4495 (define-public r-rbowtie
4502 (uri (bioconductor-uri "Rbowtie" version))
4505 "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f"))))
4506 (properties `((upstream-name . "Rbowtie")))
4507 (build-system r-build-system)
4510 (home-page "https://bioconductor.org/packages/Rbowtie/")
4511 (synopsis "R bowtie wrapper")
4513 "This package provides an R wrapper around the popular bowtie short read
4514 aligner and around SpliceMap, a de novo splice junction discovery and
4516 (license license:artistic2.0)))
4518 (define-public r-sgseq
4525 (uri (bioconductor-uri "SGSeq" version))
4528 "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
4529 (properties `((upstream-name . "SGSeq")))
4530 (build-system r-build-system)
4532 `(("r-annotationdbi" ,r-annotationdbi)
4533 ("r-biocgenerics" ,r-biocgenerics)
4534 ("r-biostrings" ,r-biostrings)
4535 ("r-genomeinfodb" ,r-genomeinfodb)
4536 ("r-genomicalignments" ,r-genomicalignments)
4537 ("r-genomicfeatures" ,r-genomicfeatures)
4538 ("r-genomicranges" ,r-genomicranges)
4539 ("r-igraph" ,r-igraph)
4540 ("r-iranges" ,r-iranges)
4541 ("r-rsamtools" ,r-rsamtools)
4542 ("r-rtracklayer" ,r-rtracklayer)
4543 ("r-runit" ,r-runit)
4544 ("r-s4vectors" ,r-s4vectors)
4545 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4546 (home-page "https://bioconductor.org/packages/SGSeq/")
4547 (synopsis "Splice event prediction and quantification from RNA-seq data")
4549 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
4550 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
4551 represented as a splice graph, which can be obtained from existing annotation
4552 or predicted from the mapped sequence reads. Splice events are identified
4553 from the graph and are quantified locally using structurally compatible reads
4554 at the start or end of each splice variant. The software includes functions
4555 for splice event prediction, quantification, visualization and
4557 (license license:artistic2.0)))
4559 (define-public r-rhisat2
4566 (uri (bioconductor-uri "Rhisat2" version))
4569 "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5"))))
4570 (properties `((upstream-name . "Rhisat2")))
4571 (build-system r-build-system)
4573 `(("which" ,which)))
4575 `(("r-genomicfeatures" ,r-genomicfeatures)
4576 ("r-genomicranges" ,r-genomicranges)
4577 ("r-sgseq" ,r-sgseq)))
4578 (home-page "https://github.com/fmicompbio/Rhisat2")
4579 (synopsis "R Wrapper for HISAT2 sequence aligner")
4581 "This package provides an R interface to the HISAT2 spliced short-read
4582 aligner by Kim et al. (2015). The package contains wrapper functions to
4583 create a genome index and to perform the read alignment to the generated
4585 (license license:gpl3)))
4587 (define-public r-quasr
4594 (uri (bioconductor-uri "QuasR" version))
4597 "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx"))))
4598 (properties `((upstream-name . "QuasR")))
4599 (build-system r-build-system)
4603 `(("r-annotationdbi" ,r-annotationdbi)
4604 ("r-biobase" ,r-biobase)
4605 ("r-biocgenerics" ,r-biocgenerics)
4606 ("r-biocmanager" ,r-biocmanager)
4607 ("r-biocparallel" ,r-biocparallel)
4608 ("r-biostrings" ,r-biostrings)
4609 ("r-bsgenome" ,r-bsgenome)
4610 ("r-genomeinfodb" ,r-genomeinfodb)
4611 ("r-genomicalignments" ,r-genomicalignments)
4612 ("r-genomicfeatures" ,r-genomicfeatures)
4613 ("r-genomicfiles" ,r-genomicfiles)
4614 ("r-genomicranges" ,r-genomicranges)
4615 ("r-iranges" ,r-iranges)
4616 ("r-rbowtie" ,r-rbowtie)
4617 ("r-rhisat2" ,r-rhisat2)
4618 ("r-rhtslib" ,r-rhtslib)
4619 ("r-rsamtools" ,r-rsamtools)
4620 ("r-rtracklayer" ,r-rtracklayer)
4621 ("r-s4vectors" ,r-s4vectors)
4622 ("r-shortread" ,r-shortread)))
4623 (home-page "https://bioconductor.org/packages/QuasR/")
4624 (synopsis "Quantify and annotate short reads in R")
4626 "This package provides a framework for the quantification and analysis of
4627 short genomic reads. It covers a complete workflow starting from raw sequence
4628 reads, over creation of alignments and quality control plots, to the
4629 quantification of genomic regions of interest.")
4630 (license license:gpl2)))
4632 (define-public r-rqc
4639 (uri (bioconductor-uri "Rqc" version))
4642 "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g"))))
4643 (properties `((upstream-name . "Rqc")))
4644 (build-system r-build-system)
4646 `(("r-biocgenerics" ,r-biocgenerics)
4647 ("r-biocparallel" ,r-biocparallel)
4648 ("r-biocstyle" ,r-biocstyle)
4649 ("r-biostrings" ,r-biostrings)
4650 ("r-biovizbase" ,r-biovizbase)
4651 ("r-genomicalignments" ,r-genomicalignments)
4652 ("r-genomicfiles" ,r-genomicfiles)
4653 ("r-ggplot2" ,r-ggplot2)
4654 ("r-iranges" ,r-iranges)
4655 ("r-knitr" ,r-knitr)
4656 ("r-markdown" ,r-markdown)
4659 ("r-reshape2" ,r-reshape2)
4660 ("r-rsamtools" ,r-rsamtools)
4661 ("r-s4vectors" ,r-s4vectors)
4662 ("r-shiny" ,r-shiny)
4663 ("r-shortread" ,r-shortread)))
4664 (home-page "https://github.com/labbcb/Rqc")
4665 (synopsis "Quality control tool for high-throughput sequencing data")
4667 "Rqc is an optimized tool designed for quality control and assessment of
4668 high-throughput sequencing data. It performs parallel processing of entire
4669 files and produces a report which contains a set of high-resolution
4671 (license license:gpl2+)))
4673 (define-public r-birewire
4680 (uri (bioconductor-uri "BiRewire" version))
4683 "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518"))))
4684 (properties `((upstream-name . "BiRewire")))
4685 (build-system r-build-system)
4687 `(("r-igraph" ,r-igraph)
4688 ("r-matrix" ,r-matrix)
4690 ("r-tsne" ,r-tsne)))
4691 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
4692 (synopsis "Tools for randomization of bipartite graphs")
4694 "This package provides functions for bipartite network rewiring through N
4695 consecutive switching steps and for the computation of the minimal number of
4696 switching steps to be performed in order to maximise the dissimilarity with
4697 respect to the original network. It includes functions for the analysis of
4698 the introduced randomness across the switching steps and several other
4699 routines to analyse the resulting networks and their natural projections.")
4700 (license license:gpl3)))
4702 (define-public r-birta
4709 (uri (bioconductor-uri "birta" version))
4712 "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2"))))
4713 (build-system r-build-system)
4715 `(("r-biobase" ,r-biobase)
4716 ("r-limma" ,r-limma)
4717 ("r-mass" ,r-mass)))
4718 (home-page "https://bioconductor.org/packages/birta")
4719 (synopsis "Bayesian inference of regulation of transcriptional activity")
4721 "Expression levels of mRNA molecules are regulated by different
4722 processes, comprising inhibition or activation by transcription factors and
4723 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
4724 Inference of Regulation of Transcriptional Activity) uses the regulatory
4725 networks of transcription factors and miRNAs together with mRNA and miRNA
4726 expression data to predict switches in regulatory activity between two
4727 conditions. A Bayesian network is used to model the regulatory structure and
4728 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
4729 (license license:gpl2+)))
4731 (define-public r-ropls
4738 (uri (bioconductor-uri "ropls" version))
4741 "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2"))))
4742 (build-system r-build-system)
4743 (propagated-inputs `(("r-biobase" ,r-biobase)))
4745 `(("r-knitr" ,r-knitr))) ; for vignettes
4746 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
4747 (synopsis "Multivariate analysis and feature selection of omics data")
4749 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
4750 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
4751 regression, classification, and feature selection of omics data where the
4752 number of variables exceeds the number of samples and with multicollinearity
4753 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
4754 separately model the variation correlated (predictive) to the factor of
4755 interest and the uncorrelated (orthogonal) variation. While performing
4756 similarly to PLS, OPLS facilitates interpretation.
4758 This package provides imlementations of PCA, PLS, and OPLS for multivariate
4759 analysis and feature selection of omics data. In addition to scores, loadings
4760 and weights plots, the package provides metrics and graphics to determine the
4761 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
4762 validity of the model by permutation testing, detect outliers, and perform
4763 feature selection (e.g. with Variable Importance in Projection or regression
4765 (license license:cecill)))
4767 (define-public r-biosigner
4769 (name "r-biosigner")
4774 (uri (bioconductor-uri "biosigner" version))
4777 "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b"))))
4778 (build-system r-build-system)
4780 `(("r-biobase" ,r-biobase)
4781 ("r-e1071" ,r-e1071)
4782 ("r-randomforest" ,r-randomforest)
4783 ("r-ropls" ,r-ropls)))
4785 `(("r-knitr" ,r-knitr)
4786 ("r-rmarkdown" ,r-rmarkdown)
4787 ("pandoc" ,ghc-pandoc)
4788 ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
4789 (home-page "https://bioconductor.org/packages/biosigner/")
4790 (synopsis "Signature discovery from omics data")
4792 "Feature selection is critical in omics data analysis to extract
4793 restricted and meaningful molecular signatures from complex and high-dimension
4794 data, and to build robust classifiers. This package implements a method to
4795 assess the relevance of the variables for the prediction performances of the
4796 classifier. The approach can be run in parallel with the PLS-DA, Random
4797 Forest, and SVM binary classifiers. The signatures and the corresponding
4798 'restricted' models are returned, enabling future predictions on new
4800 (license license:cecill)))
4802 (define-public r-annotatr
4809 (uri (bioconductor-uri "annotatr" version))
4812 "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f"))))
4813 (build-system r-build-system)
4815 `(("r-annotationdbi" ,r-annotationdbi)
4816 ("r-annotationhub" ,r-annotationhub)
4817 ("r-dplyr" ,r-dplyr)
4818 ("r-genomeinfodb" ,r-genomeinfodb)
4819 ("r-genomicfeatures" ,r-genomicfeatures)
4820 ("r-genomicranges" ,r-genomicranges)
4821 ("r-ggplot2" ,r-ggplot2)
4822 ("r-iranges" ,r-iranges)
4823 ("r-readr" ,r-readr)
4824 ("r-regioner" ,r-regioner)
4825 ("r-reshape2" ,r-reshape2)
4826 ("r-rtracklayer" ,r-rtracklayer)
4827 ("r-s4vectors" ,r-s4vectors)))
4828 (home-page "https://bioconductor.org/packages/annotatr/")
4829 (synopsis "Annotation of genomic regions to genomic annotations")
4831 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
4832 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
4833 to investigate the intersecting genomic annotations. Such annotations include
4834 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
4835 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
4836 enhancers. The annotatr package provides an easy way to summarize and
4837 visualize the intersection of genomic sites/regions with genomic
4839 (license license:gpl3)))
4841 (define-public r-rsubread
4848 (uri (bioconductor-uri "Rsubread" version))
4851 "0nnfh4hnrs5kd72m8c50cidbsxjz12szw2vynpmg8q0wpd99q550"))))
4852 (properties `((upstream-name . "Rsubread")))
4853 (build-system r-build-system)
4854 (inputs `(("zlib" ,zlib)))
4855 (home-page "https://bioconductor.org/packages/Rsubread/")
4856 (synopsis "Subread sequence alignment and counting for R")
4858 "This package provides tools for alignment, quantification and analysis
4859 of second and third generation sequencing data. It includes functionality for
4860 read mapping, read counting, SNP calling, structural variant detection and
4861 gene fusion discovery. It can be applied to all major sequencing techologies
4862 and to both short and long sequence reads.")
4863 (license license:gpl3)))
4865 (define-public r-flowutils
4867 (name "r-flowutils")
4872 (uri (bioconductor-uri "flowUtils" version))
4875 "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm"))))
4876 (properties `((upstream-name . "flowUtils")))
4877 (build-system r-build-system)
4879 `(("r-biobase" ,r-biobase)
4880 ("r-corpcor" ,r-corpcor)
4881 ("r-flowcore" ,r-flowcore)
4882 ("r-graph" ,r-graph)
4883 ("r-runit" ,r-runit)
4885 (home-page "https://github.com/jspidlen/flowUtils")
4886 (synopsis "Utilities for flow cytometry")
4888 "This package provides utilities for flow cytometry data.")
4889 (license license:artistic2.0)))
4891 (define-public r-consensusclusterplus
4893 (name "r-consensusclusterplus")
4898 (uri (bioconductor-uri "ConsensusClusterPlus" version))
4901 "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8"))))
4903 `((upstream-name . "ConsensusClusterPlus")))
4904 (build-system r-build-system)
4907 ("r-biobase" ,r-biobase)
4908 ("r-cluster" ,r-cluster)))
4909 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
4910 (synopsis "Clustering algorithm")
4912 "This package provides an implementation of an algorithm for determining
4913 cluster count and membership by stability evidence in unsupervised analysis.")
4914 (license license:gpl2)))
4916 (define-public r-flowcore
4923 (uri (bioconductor-uri "flowCore" version))
4926 "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan"))))
4927 (properties `((upstream-name . "flowCore")))
4928 (build-system r-build-system)
4931 ("r-biobase" ,r-biobase)
4932 ("r-biocgenerics" ,r-biocgenerics)
4933 ("r-corpcor" ,r-corpcor)
4934 ("r-graph" ,r-graph)
4936 ("r-matrixstats" ,r-matrixstats)
4938 ("r-rrcov" ,r-rrcov)))
4939 (home-page "https://bioconductor.org/packages/flowCore")
4940 (synopsis "Basic structures for flow cytometry data")
4942 "This package provides S4 data structures and basic functions to deal
4943 with flow cytometry data.")
4944 (license license:artistic2.0)))
4946 (define-public r-flowmeans
4948 (name "r-flowmeans")
4953 (uri (bioconductor-uri "flowMeans" version))
4956 "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2"))))
4957 (properties `((upstream-name . "flowMeans")))
4958 (build-system r-build-system)
4960 `(("r-biobase" ,r-biobase)
4961 ("r-feature" ,r-feature)
4962 ("r-flowcore" ,r-flowcore)
4963 ("r-rrcov" ,r-rrcov)))
4964 (home-page "https://bioconductor.org/packages/flowMeans")
4965 (synopsis "Non-parametric flow cytometry data gating")
4967 "This package provides tools to identify cell populations in Flow
4968 Cytometry data using non-parametric clustering and segmented-regression-based
4969 change point detection.")
4970 (license license:artistic2.0)))
4972 (define-public r-flowsom
4979 (uri (bioconductor-uri "FlowSOM" version))
4982 "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l"))))
4983 (properties `((upstream-name . "FlowSOM")))
4984 (build-system r-build-system)
4986 `(("r-biocgenerics" ,r-biocgenerics)
4987 ("r-consensusclusterplus" ,r-consensusclusterplus)
4988 ("r-flowcore" ,r-flowcore)
4989 ("r-flowutils" ,r-flowutils)
4990 ("r-igraph" ,r-igraph)
4993 (home-page "https://bioconductor.org/packages/FlowSOM/")
4994 (synopsis "Visualize and interpret cytometry data")
4996 "FlowSOM offers visualization options for cytometry data, by using
4997 self-organizing map clustering and minimal spanning trees.")
4998 (license license:gpl2+)))
5000 (define-public r-mixomics
5007 (uri (bioconductor-uri "mixOmics" version))
5010 "1f08jx35amn3sfcmqb96mjxxsm6dnpzhff625z758x1992wj4zsk"))))
5011 (properties `((upstream-name . "mixOmics")))
5012 (build-system r-build-system)
5014 `(("r-corpcor" ,r-corpcor)
5015 ("r-dplyr" ,r-dplyr)
5016 ("r-ellipse" ,r-ellipse)
5017 ("r-ggplot2" ,r-ggplot2)
5018 ("r-gridextra" ,r-gridextra)
5019 ("r-igraph" ,r-igraph)
5020 ("r-lattice" ,r-lattice)
5022 ("r-matrixstats" ,r-matrixstats)
5023 ("r-rarpack" ,r-rarpack)
5024 ("r-rcolorbrewer" ,r-rcolorbrewer)
5025 ("r-reshape2" ,r-reshape2)
5026 ("r-tidyr" ,r-tidyr)))
5027 (home-page "http://www.mixOmics.org")
5028 (synopsis "Multivariate methods for exploration of biological datasets")
5030 "mixOmics offers a wide range of multivariate methods for the exploration
5031 and integration of biological datasets with a particular focus on variable
5032 selection. The package proposes several sparse multivariate models we have
5033 developed to identify the key variables that are highly correlated, and/or
5034 explain the biological outcome of interest. The data that can be analysed
5035 with mixOmics may come from high throughput sequencing technologies, such as
5036 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
5037 also beyond the realm of omics (e.g. spectral imaging). The methods
5038 implemented in mixOmics can also handle missing values without having to
5039 delete entire rows with missing data.")
5040 (license license:gpl2+)))
5042 (define-public r-depecher
5049 (uri (bioconductor-uri "DepecheR" version))
5052 "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h"))))
5053 (properties `((upstream-name . "DepecheR")))
5054 (build-system r-build-system)
5057 (modify-phases %standard-phases
5058 (add-after 'unpack 'fix-syntax-error
5060 (substitute* "src/Makevars"
5064 `(("r-beanplot" ,r-beanplot)
5065 ("r-biocparallel" ,r-biocparallel)
5066 ("r-dosnow" ,r-dosnow)
5067 ("r-dplyr" ,r-dplyr)
5068 ("r-foreach" ,r-foreach)
5069 ("r-ggplot2" ,r-ggplot2)
5070 ("r-gplots" ,r-gplots)
5072 ("r-matrixstats" ,r-matrixstats)
5073 ("r-mixomics" ,r-mixomics)
5074 ("r-moments" ,r-moments)
5076 ("r-rcppeigen" ,r-rcppeigen)
5077 ("r-reshape2" ,r-reshape2)
5078 ("r-viridis" ,r-viridis)))
5079 (home-page "https://bioconductor.org/packages/DepecheR/")
5080 (synopsis "Identify traits of clusters in high-dimensional entities")
5082 "The purpose of this package is to identify traits in a dataset that can
5083 separate groups. This is done on two levels. First, clustering is performed,
5084 using an implementation of sparse K-means. Secondly, the generated clusters
5085 are used to predict outcomes of groups of individuals based on their
5086 distribution of observations in the different clusters. As certain clusters
5087 with separating information will be identified, and these clusters are defined
5088 by a sparse number of variables, this method can reduce the complexity of
5089 data, to only emphasize the data that actually matters.")
5090 (license license:expat)))
5092 (define-public r-rcistarget
5094 (name "r-rcistarget")
5099 (uri (bioconductor-uri "RcisTarget" version))
5102 "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd"))))
5103 (properties `((upstream-name . "RcisTarget")))
5104 (build-system r-build-system)
5106 `(("r-aucell" ,r-aucell)
5107 ("r-biocgenerics" ,r-biocgenerics)
5108 ("r-data-table" ,r-data-table)
5109 ("r-feather" ,r-feather)
5110 ("r-gseabase" ,r-gseabase)
5111 ("r-r-utils" ,r-r-utils)
5112 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5113 (home-page "https://aertslab.org/#scenic")
5114 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
5116 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
5117 over-represented on a gene list. In a first step, RcisTarget selects DNA
5118 motifs that are significantly over-represented in the surroundings of the
5119 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
5120 achieved by using a database that contains genome-wide cross-species rankings
5121 for each motif. The motifs that are then annotated to TFs and those that have
5122 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
5123 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
5124 genes in the gene-set that are ranked above the leading edge).")
5125 (license license:gpl3)))
5127 (define-public r-cicero
5134 (uri (bioconductor-uri "cicero" version))
5137 "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr"))))
5138 (build-system r-build-system)
5140 `(("r-assertthat" ,r-assertthat)
5141 ("r-biobase" ,r-biobase)
5142 ("r-biocgenerics" ,r-biocgenerics)
5143 ("r-data-table" ,r-data-table)
5144 ("r-dplyr" ,r-dplyr)
5146 ("r-genomicranges" ,r-genomicranges)
5147 ("r-ggplot2" ,r-ggplot2)
5148 ("r-glasso" ,r-glasso)
5150 ("r-igraph" ,r-igraph)
5151 ("r-iranges" ,r-iranges)
5152 ("r-matrix" ,r-matrix)
5153 ("r-monocle" ,r-monocle)
5155 ("r-reshape2" ,r-reshape2)
5156 ("r-s4vectors" ,r-s4vectors)
5157 ("r-stringr" ,r-stringr)
5158 ("r-tibble" ,r-tibble)
5159 ("r-vgam" ,r-vgam)))
5160 (home-page "https://bioconductor.org/packages/cicero/")
5161 (synopsis "Predict cis-co-accessibility from single-cell data")
5163 "Cicero computes putative cis-regulatory maps from single-cell chromatin
5164 accessibility data. It also extends the monocle package for use in chromatin
5165 accessibility data.")
5166 (license license:expat)))
5168 ;; This is the latest commit on the "monocle3" branch.
5169 (define-public r-cicero-monocle3
5170 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
5172 (package (inherit r-cicero)
5173 (name "r-cicero-monocle3")
5174 (version (git-version "1.3.2" revision commit))
5179 (url "https://github.com/cole-trapnell-lab/cicero-release.git")
5181 (file-name (git-file-name name version))
5184 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
5186 `(("r-monocle3" ,r-monocle3)
5187 ,@(alist-delete "r-monocle"
5188 (package-propagated-inputs r-cicero)))))))
5190 (define-public r-cistopic
5191 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
5195 (version (git-version "0.2.1" revision commit))
5200 (url "https://github.com/aertslab/cisTopic.git")
5202 (file-name (git-file-name name version))
5205 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
5206 (build-system r-build-system)
5208 `(("r-aucell" ,r-aucell)
5209 ("r-data-table" ,r-data-table)
5210 ("r-dplyr" ,r-dplyr)
5211 ("r-dosnow" ,r-dosnow)
5213 ("r-feather" ,r-feather)
5214 ("r-fitdistrplus" ,r-fitdistrplus)
5215 ("r-genomicranges" ,r-genomicranges)
5216 ("r-ggplot2" ,r-ggplot2)
5218 ("r-matrix" ,r-matrix)
5220 ("r-rcistarget" ,r-rcistarget)
5221 ("r-rtracklayer" ,r-rtracklayer)
5222 ("r-s4vectors" ,r-s4vectors)))
5223 (home-page "https://github.com/aertslab/cisTopic")
5224 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
5226 "The sparse nature of single cell epigenomics data can be overruled using
5227 probabilistic modelling methods such as @dfn{Latent Dirichlet
5228 Allocation} (LDA). This package allows the probabilistic modelling of
5229 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
5230 includes functionalities to identify cell states based on the contribution of
5231 cisTopics and explore the nature and regulatory proteins driving them.")
5232 (license license:gpl3))))