1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2018 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2018 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 build-system r)
26 #:use-module (gnu packages)
27 #:use-module (gnu packages bioinformatics)
28 #:use-module (gnu packages cran)
29 #:use-module (gnu packages compression)
30 #:use-module (gnu packages graph)
31 #:use-module (gnu packages maths)
32 #:use-module (gnu packages statistics)
33 #:use-module (gnu packages web))
35 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
37 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
41 ;; We cannot use bioconductor-uri here because this tarball is
42 ;; located under "data/annotation/" instead of "bioc/".
43 (uri (string-append "https://www.bioconductor.org/packages/"
44 "release/data/annotation/src/contrib/"
45 "BSgenome.Dmelanogaster.UCSC.dm6_"
49 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
51 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
52 (build-system r-build-system)
53 ;; As this package provides little more than a very large data file it
54 ;; doesn't make sense to build substitutes.
55 (arguments `(#:substitutable? #f))
57 `(("r-bsgenome" ,r-bsgenome)))
59 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
60 (synopsis "Full genome sequences for Fly")
62 "This package provides full genome sequences for Drosophila
63 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
65 (license license:artistic2.0)))
67 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
69 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
73 ;; We cannot use bioconductor-uri here because this tarball is
74 ;; located under "data/annotation/" instead of "bioc/".
75 (uri (string-append "http://www.bioconductor.org/packages/"
76 "release/data/annotation/src/contrib/"
77 "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
81 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
83 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
84 (build-system r-build-system)
86 `(("r-bsgenome" ,r-bsgenome)
87 ("r-bsgenome-dmelanogaster-ucsc-dm3"
88 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
89 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
90 (synopsis "Full masked genome sequences for Fly")
92 "This package provides full masked genome sequences for Drosophila
93 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
94 Biostrings objects. The sequences are the same as in
95 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
96 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
97 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
98 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
99 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
100 (license license:artistic2.0)))
102 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
104 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
108 ;; We cannot use bioconductor-uri here because this tarball is
109 ;; located under "data/annotation/" instead of "bioc/".
110 (uri (string-append "http://www.bioconductor.org/packages/"
111 "release/data/annotation/src/contrib/"
112 "BSgenome.Hsapiens.UCSC.hg19.masked_"
116 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
118 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
119 (build-system r-build-system)
121 `(("r-bsgenome" ,r-bsgenome)
122 ("r-bsgenome-hsapiens-ucsc-hg19"
123 ,r-bsgenome-hsapiens-ucsc-hg19)))
124 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
125 (synopsis "Full masked genome sequences for Homo sapiens")
127 "This package provides full genome sequences for Homo sapiens (Human) as
128 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
129 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
130 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
131 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
132 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
133 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
135 (license license:artistic2.0)))
137 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
139 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
143 ;; We cannot use bioconductor-uri here because this tarball is
144 ;; located under "data/annotation/" instead of "bioc/".
145 (uri (string-append "http://www.bioconductor.org/packages/"
146 "release/data/annotation/src/contrib/"
147 "BSgenome.Mmusculus.UCSC.mm9.masked_"
151 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
153 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
154 (build-system r-build-system)
156 `(("r-bsgenome" ,r-bsgenome)
157 ("r-bsgenome-mmusculus-ucsc-mm9"
158 ,r-bsgenome-mmusculus-ucsc-mm9)))
159 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
160 (synopsis "Full masked genome sequences for Mouse")
162 "This package provides full genome sequences for Mus musculus (Mouse) as
163 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
164 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
165 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
166 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
167 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
168 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
170 (license license:artistic2.0)))
172 (define-public r-genelendatabase
174 (name "r-genelendatabase")
179 ;; We cannot use bioconductor-uri here because this tarball is
180 ;; located under "data/experiment/" instead of "bioc/".
181 (uri (string-append "https://bioconductor.org/packages/"
182 "release/data/experiment/src/contrib"
183 "/geneLenDataBase_" version ".tar.gz"))
186 "07mmmn53kb7v14msc13dsbm8ghssbvwcrhifrk15hn37bw2p4ja5"))))
188 `((upstream-name . "geneLenDataBase")))
189 (build-system r-build-system)
191 `(("r-rtracklayer" ,r-rtracklayer)
192 ("r-genomicfeatures" ,r-genomicfeatures)))
193 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
194 (synopsis "Lengths of mRNA transcripts for a number of genomes")
196 "This package provides the lengths of mRNA transcripts for a number of
197 genomes and gene ID formats, largely based on the UCSC table browser.")
198 (license license:lgpl2.0+)))
201 (define-public r-hpar
208 (uri (bioconductor-uri "hpar" version))
211 "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388"))))
212 (build-system r-build-system)
213 (home-page "https://bioconductor.org/packages/hpar/")
214 (synopsis "Human Protein Atlas in R")
215 (description "This package provides a simple interface to and data from
216 the Human Protein Atlas project.")
217 (license license:artistic2.0)))
219 (define-public r-regioner
226 (uri (bioconductor-uri "regioneR" version))
229 "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb"))))
230 (properties `((upstream-name . "regioneR")))
231 (build-system r-build-system)
233 `(("r-memoise" ,r-memoise)
234 ("r-genomicranges" ,r-genomicranges)
235 ("r-bsgenome" ,r-bsgenome)
236 ("r-rtracklayer" ,r-rtracklayer)
237 ("r-genomeinfodb" ,r-genomeinfodb)
238 ("r-iranges" ,r-iranges)
239 ("r-s4vectors" ,r-s4vectors)))
240 (home-page "https://bioconductor.org/packages/regioneR/")
241 (synopsis "Association analysis of genomic regions")
242 (description "This package offers a statistical framework based on
243 customizable permutation tests to assess the association between genomic
244 region sets and other genomic features.")
245 (license license:artistic2.0)))
247 (define-public r-diffbind
254 (uri (bioconductor-uri "DiffBind" version))
257 "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish"))))
258 (properties `((upstream-name . "DiffBind")))
259 (build-system r-build-system)
264 ("r-biocparallel" ,r-biocparallel)
265 ("r-deseq2" ,r-deseq2)
268 ("r-genomicalignments" ,r-genomicalignments)
269 ("r-genomicranges" ,r-genomicranges)
270 ("r-ggplot2" ,r-ggplot2)
271 ("r-ggrepel" ,r-ggrepel)
272 ("r-gplots" ,r-gplots)
273 ("r-iranges" ,r-iranges)
274 ("r-lattice" ,r-lattice)
276 ("r-locfit" ,r-locfit)
277 ("r-rcolorbrewer" , r-rcolorbrewer)
279 ("r-rsamtools" ,r-rsamtools)
280 ("r-s4vectors" ,r-s4vectors)
281 ("r-summarizedexperiment" ,r-summarizedexperiment)
282 ("r-systempiper" ,r-systempiper)
283 ("r-zlibbioc" ,r-zlibbioc)))
284 (home-page "http://bioconductor.org/packages/DiffBind")
285 (synopsis "Differential binding analysis of ChIP-Seq peak data")
287 "This package computes differentially bound sites from multiple
288 ChIP-seq experiments using affinity (quantitative) data. Also enables
289 occupancy (overlap) analysis and plotting functions.")
290 (license license:artistic2.0)))
292 (define-public r-ripseeker
299 (uri (bioconductor-uri "RIPSeeker" version))
302 "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi"))))
303 (properties `((upstream-name . "RIPSeeker")))
304 (build-system r-build-system)
306 `(("r-s4vectors" ,r-s4vectors)
307 ("r-iranges" ,r-iranges)
308 ("r-genomicranges" ,r-genomicranges)
309 ("r-summarizedexperiment" ,r-summarizedexperiment)
310 ("r-rsamtools" ,r-rsamtools)
311 ("r-genomicalignments" ,r-genomicalignments)
312 ("r-rtracklayer" ,r-rtracklayer)))
313 (home-page "http://bioconductor.org/packages/RIPSeeker")
315 "Identifying protein-associated transcripts from RIP-seq experiments")
317 "This package infers and discriminates RIP peaks from RIP-seq alignments
318 using two-state HMM with negative binomial emission probability. While
319 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
320 a suite of bioinformatics tools integrated within this self-contained software
321 package comprehensively addressing issues ranging from post-alignments
322 processing to visualization and annotation.")
323 (license license:gpl2)))
325 (define-public r-multtest
332 (uri (bioconductor-uri "multtest" version))
335 "11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0"))))
336 (build-system r-build-system)
338 `(("r-survival" ,r-survival)
339 ("r-biocgenerics" ,r-biocgenerics)
340 ("r-biobase" ,r-biobase)
342 (home-page "http://bioconductor.org/packages/multtest")
343 (synopsis "Resampling-based multiple hypothesis testing")
345 "This package can do non-parametric bootstrap and permutation
346 resampling-based multiple testing procedures (including empirical Bayes
347 methods) for controlling the family-wise error rate (FWER), generalized
348 family-wise error rate (gFWER), tail probability of the proportion of
349 false positives (TPPFP), and false discovery rate (FDR). Several choices
350 of bootstrap-based null distribution are implemented (centered, centered
351 and scaled, quantile-transformed). Single-step and step-wise methods are
352 available. Tests based on a variety of T- and F-statistics (including
353 T-statistics based on regression parameters from linear and survival models
354 as well as those based on correlation parameters) are included. When probing
355 hypotheses with T-statistics, users may also select a potentially faster null
356 distribution which is multivariate normal with mean zero and variance
357 covariance matrix derived from the vector influence function. Results are
358 reported in terms of adjusted P-values, confidence regions and test statistic
359 cutoffs. The procedures are directly applicable to identifying differentially
360 expressed genes in DNA microarray experiments.")
361 (license license:lgpl3)))
363 (define-public r-graph
369 (uri (bioconductor-uri "graph" version))
372 "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759"))))
373 (build-system r-build-system)
375 `(("r-biocgenerics" ,r-biocgenerics)))
376 (home-page "https://bioconductor.org/packages/graph")
377 (synopsis "Handle graph data structures in R")
379 "This package implements some simple graph handling capabilities for R.")
380 (license license:artistic2.0)))
382 (define-public r-chippeakanno
384 (name "r-chippeakanno")
389 (uri (bioconductor-uri "ChIPpeakAnno" version))
392 "1cn1hfc3nvsf2n3563lkmvwjxfbiygx7f84zk683p89gy7zi1gyj"))))
393 (properties `((upstream-name . "ChIPpeakAnno")))
394 (build-system r-build-system)
396 `(("r-biocgenerics" ,r-biocgenerics)
397 ("r-biostrings" ,r-biostrings)
398 ("r-delayedarray" ,r-delayedarray)
400 ("r-biomart" ,r-biomart)
401 ("r-bsgenome" ,r-bsgenome)
402 ("r-genomicfeatures" ,r-genomicfeatures)
403 ("r-genomicranges" ,r-genomicranges)
404 ("r-genomeinfodb" ,r-genomeinfodb)
405 ("r-iranges" ,r-iranges)
406 ("r-matrixstats" ,r-matrixstats)
407 ("r-annotationdbi" ,r-annotationdbi)
409 ("r-multtest" ,r-multtest)
412 ("r-biocinstaller" ,r-biocinstaller)
413 ("r-regioner" ,r-regioner)
415 ("r-ensembldb" ,r-ensembldb)
416 ("r-biobase" ,r-biobase)
417 ("r-s4vectors" ,r-s4vectors)
418 ("r-seqinr" ,r-seqinr)
420 ("r-genomicalignments" ,r-genomicalignments)
421 ("r-summarizedexperiment" ,r-summarizedexperiment)
422 ("r-rsamtools" ,r-rsamtools)
423 ("r-venndiagram" ,r-venndiagram)))
424 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
425 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
427 "The package includes functions to retrieve the sequences around the peak,
428 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
429 custom features such as most conserved elements and other transcription factor
430 binding sites supplied by users. Starting 2.0.5, new functions have been added
431 for finding the peaks with bi-directional promoters with summary statistics
432 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
433 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
434 enrichedGO (addGeneIDs).")
435 (license license:gpl2+)))
437 (define-public r-marray
443 (uri (bioconductor-uri "marray" version))
445 (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d"))))
446 (build-system r-build-system)
448 `(("r-limma" ,r-limma)))
449 (home-page "http://bioconductor.org/packages/marray")
450 (synopsis "Exploratory analysis for two-color spotted microarray data")
451 (description "This package contains class definitions for two-color spotted
452 microarray data. It also includes fuctions for data input, diagnostic plots,
453 normalization and quality checking.")
454 (license license:lgpl2.0+)))
456 (define-public r-cghbase
462 (uri (bioconductor-uri "CGHbase" version))
464 (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq"))))
465 (properties `((upstream-name . "CGHbase")))
466 (build-system r-build-system)
468 `(("r-biobase" ,r-biobase)
469 ("r-marray" ,r-marray)))
470 (home-page "http://bioconductor.org/packages/CGHbase")
471 (synopsis "Base functions and classes for arrayCGH data analysis")
472 (description "This package contains functions and classes that are needed by
473 the @code{arrayCGH} packages.")
474 (license license:gpl2+)))
476 (define-public r-cghcall
482 (uri (bioconductor-uri "CGHcall" version))
484 (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz"))))
485 (properties `((upstream-name . "CGHcall")))
486 (build-system r-build-system)
488 `(("r-biobase" ,r-biobase)
489 ("r-cghbase" ,r-cghbase)
490 ("r-impute" ,r-impute)
491 ("r-dnacopy" ,r-dnacopy)
492 ("r-snowfall" ,r-snowfall)))
493 (home-page "http://bioconductor.org/packages/CGHcall")
494 (synopsis "Base functions and classes for arrayCGH data analysis")
495 (description "This package contains functions and classes that are needed by
496 @code{arrayCGH} packages.")
497 (license license:gpl2+)))
499 (define-public r-qdnaseq
505 (uri (bioconductor-uri "QDNAseq" version))
507 (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd"))))
508 (properties `((upstream-name . "QDNAseq")))
509 (build-system r-build-system)
511 `(("r-biobase" ,r-biobase)
512 ("r-biocparallel" ,r-biocparallel)
513 ("r-cghbase" ,r-cghbase)
514 ("r-cghcall" ,r-cghcall)
515 ("r-dnacopy" ,r-dnacopy)
516 ("r-genomicranges" ,r-genomicranges)
517 ("r-iranges" ,r-iranges)
518 ("r-matrixstats" ,r-matrixstats)
519 ("r-r-utils" ,r-r-utils)
520 ("r-rsamtools" ,r-rsamtools)))
521 (home-page "http://bioconductor.org/packages/QDNAseq")
522 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
523 (description "The genome is divided into non-overlapping fixed-sized bins,
524 number of sequence reads in each counted, adjusted with a simultaneous
525 two-dimensional loess correction for sequence mappability and GC content, and
526 filtered to remove spurious regions in the genome. Downstream steps of
527 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
529 (license license:gpl2+)))
531 (define-public r-bayseq
538 (uri (bioconductor-uri "baySeq" version))
541 "0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg"))))
542 (properties `((upstream-name . "baySeq")))
543 (build-system r-build-system)
545 `(("r-abind" ,r-abind)
547 ("r-genomicranges" ,r-genomicranges)))
548 (home-page "https://bioconductor.org/packages/baySeq/")
549 (synopsis "Bayesian analysis of differential expression patterns in count data")
551 "This package identifies differential expression in high-throughput count
552 data, such as that derived from next-generation sequencing machines,
553 calculating estimated posterior likelihoods of differential expression (or
554 more complex hypotheses) via empirical Bayesian methods.")
555 (license license:gpl3)))
557 (define-public r-chipcomp
564 (uri (bioconductor-uri "ChIPComp" version))
567 "0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs"))))
568 (properties `((upstream-name . "ChIPComp")))
569 (build-system r-build-system)
571 `(("r-biocgenerics" ,r-biocgenerics)
572 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
573 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
574 ("r-genomeinfodb" ,r-genomeinfodb)
575 ("r-genomicranges" ,r-genomicranges)
576 ("r-iranges" ,r-iranges)
578 ("r-rsamtools" ,r-rsamtools)
579 ("r-rtracklayer" ,r-rtracklayer)
580 ("r-s4vectors" ,r-s4vectors)))
581 (home-page "https://bioconductor.org/packages/ChIPComp")
582 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
584 "ChIPComp implements a statistical method for quantitative comparison of
585 multiple ChIP-seq datasets. It detects differentially bound sharp binding
586 sites across multiple conditions considering matching control in ChIP-seq
588 ;; Any version of the GPL.
589 (license license:gpl3+)))
591 (define-public r-riboprofiling
593 (name "r-riboprofiling")
598 (uri (bioconductor-uri "RiboProfiling" version))
601 "04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0"))))
602 (properties `((upstream-name . "RiboProfiling")))
603 (build-system r-build-system)
605 `(("r-biocgenerics" ,r-biocgenerics)
606 ("r-biostrings" ,r-biostrings)
607 ("r-data-table" ,r-data-table)
608 ("r-genomeinfodb" ,r-genomeinfodb)
609 ("r-genomicalignments" ,r-genomicalignments)
610 ("r-genomicfeatures" ,r-genomicfeatures)
611 ("r-genomicranges" ,r-genomicranges)
613 ("r-ggplot2" ,r-ggplot2)
614 ("r-iranges" ,r-iranges)
616 ("r-reshape2" ,r-reshape2)
617 ("r-rsamtools" ,r-rsamtools)
618 ("r-rtracklayer" ,r-rtracklayer)
619 ("r-s4vectors" ,r-s4vectors)
620 ("r-sqldf" ,r-sqldf)))
621 (home-page "https://bioconductor.org/packages/RiboProfiling/")
622 (synopsis "Ribosome profiling data analysis")
623 (description "Starting with a BAM file, this package provides the
624 necessary functions for quality assessment, read start position recalibration,
625 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
626 of count data: pairs, log fold-change, codon frequency and coverage
627 assessment, principal component analysis on codon coverage.")
628 (license license:gpl3)))
630 (define-public r-riboseqr
637 (uri (bioconductor-uri "riboSeqR" version))
640 "0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn"))))
641 (properties `((upstream-name . "riboSeqR")))
642 (build-system r-build-system)
644 `(("r-abind" ,r-abind)
645 ("r-bayseq" ,r-bayseq)
646 ("r-genomeinfodb" ,r-genomeinfodb)
647 ("r-genomicranges" ,r-genomicranges)
648 ("r-iranges" ,r-iranges)
649 ("r-rsamtools" ,r-rsamtools)
650 ("r-seqlogo" ,r-seqlogo)))
651 (home-page "https://bioconductor.org/packages/riboSeqR/")
652 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
654 "This package provides plotting functions, frameshift detection and
655 parsing of genetic sequencing data from ribosome profiling experiments.")
656 (license license:gpl3)))
658 (define-public r-interactionset
660 (name "r-interactionset")
665 (uri (bioconductor-uri "InteractionSet" version))
668 "0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n"))))
670 `((upstream-name . "InteractionSet")))
671 (build-system r-build-system)
673 `(("r-biocgenerics" ,r-biocgenerics)
674 ("r-genomeinfodb" ,r-genomeinfodb)
675 ("r-genomicranges" ,r-genomicranges)
676 ("r-iranges" ,r-iranges)
677 ("r-matrix" ,r-matrix)
679 ("r-s4vectors" ,r-s4vectors)
680 ("r-summarizedexperiment" ,r-summarizedexperiment)))
681 (home-page "https://bioconductor.org/packages/InteractionSet")
682 (synopsis "Base classes for storing genomic interaction data")
684 "This packages provides the @code{GInteractions},
685 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
686 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
688 (license license:gpl3)))
690 (define-public r-genomicinteractions
692 (name "r-genomicinteractions")
697 (uri (bioconductor-uri "GenomicInteractions" version))
700 "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q"))))
702 `((upstream-name . "GenomicInteractions")))
703 (build-system r-build-system)
705 `(("r-biobase" ,r-biobase)
706 ("r-biocgenerics" ,r-biocgenerics)
707 ("r-data-table" ,r-data-table)
709 ("r-genomeinfodb" ,r-genomeinfodb)
710 ("r-genomicranges" ,r-genomicranges)
711 ("r-ggplot2" ,r-ggplot2)
712 ("r-gridextra" ,r-gridextra)
714 ("r-igraph" ,r-igraph)
715 ("r-interactionset" ,r-interactionset)
716 ("r-iranges" ,r-iranges)
717 ("r-rsamtools" ,r-rsamtools)
718 ("r-rtracklayer" ,r-rtracklayer)
719 ("r-s4vectors" ,r-s4vectors)
720 ("r-stringr" ,r-stringr)))
721 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
722 (synopsis "R package for handling genomic interaction data")
724 "This R package provides tools for handling genomic interaction data,
725 such as ChIA-PET/Hi-C, annotating genomic features with interaction
726 information and producing various plots and statistics.")
727 (license license:gpl3)))
736 (uri (bioconductor-uri "ctc" version))
739 "0sadplm4n9n3z6inmn6y3d6qbr4hllljqh700x5fygrnfacnckk9"))))
740 (build-system r-build-system)
741 (propagated-inputs `(("r-amap" ,r-amap)))
742 (home-page "https://bioconductor.org/packages/ctc/")
743 (synopsis "Cluster and tree conversion")
745 "This package provides tools for exporting and importing classification
746 trees and clusters to other programs.")
747 (license license:gpl2)))
749 (define-public r-goseq
756 (uri (bioconductor-uri "goseq" version))
759 "0xmbb8ma32lrfy810r82y34gkspq4fqiqxykic9j4rq9rg9n9x2l"))))
760 (build-system r-build-system)
762 `(("r-annotationdbi" ,r-annotationdbi)
763 ("r-biasedurn" ,r-biasedurn)
764 ("r-biocgenerics" ,r-biocgenerics)
765 ("r-genelendatabase" ,r-genelendatabase)
768 (home-page "https://bioconductor.org/packages/goseq/")
769 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
771 "This package provides tools to detect Gene Ontology and/or other user
772 defined categories which are over/under represented in RNA-seq data.")
773 (license license:lgpl2.0+)))
775 (define-public r-glimma
782 (uri (bioconductor-uri "Glimma" version))
785 "0kfia60vrlys6amdchdix01iwbkwyb7nfjqn5hczsxp8rhmbg25s"))))
786 (properties `((upstream-name . "Glimma")))
787 (build-system r-build-system)
789 `(("r-edger" ,r-edger)
790 ("r-jsonlite" ,r-jsonlite)
791 ("r-s4vectors" ,r-s4vectors)))
792 (home-page "https://github.com/Shians/Glimma")
793 (synopsis "Interactive HTML graphics")
795 "This package generates interactive visualisations for analysis of
796 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
797 HTML page. The interactions are built on top of the popular static
798 representations of analysis results in order to provide additional
800 (license license:lgpl3)))
802 (define-public r-rots
809 (uri (bioconductor-uri "ROTS" version))
812 "12jvdqanyk86ihpcylp105zip22y0gkbksmyxy00q7iad0jhaqp3"))))
813 (properties `((upstream-name . "ROTS")))
814 (build-system r-build-system)
816 `(("r-biobase" ,r-biobase)
818 (home-page "https://bioconductor.org/packages/ROTS/")
819 (synopsis "Reproducibility-Optimized Test Statistic")
821 "This package provides tools for calculating the
822 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
824 (license license:gpl2+)))
826 (define-public r-inspect
833 (uri (bioconductor-uri "INSPEcT" version))
836 "1gk0pwyimkswrvgb2xr3c2zy4myi448a2shr5ap65rq9pcpp0l8p"))))
837 (properties `((upstream-name . "INSPEcT")))
838 (build-system r-build-system)
840 `(("r-biobase" ,r-biobase)
841 ("r-biocgenerics" ,r-biocgenerics)
842 ("r-biocparallel" ,r-biocparallel)
843 ("r-desolve" ,r-desolve)
844 ("r-genomicalignments" ,r-genomicalignments)
845 ("r-genomicfeatures" ,r-genomicfeatures)
846 ("r-genomicranges" ,r-genomicranges)
847 ("r-iranges" ,r-iranges)
848 ("r-preprocesscore" ,r-preprocesscore)
850 ("r-rootsolve" ,r-rootsolve)
851 ("r-rsamtools" ,r-rsamtools)
852 ("r-s4vectors" ,r-s4vectors)))
853 (home-page "https://bioconductor.org/packages/INSPEcT")
854 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
856 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
857 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
858 order to evaluate synthesis, processing and degradation rates and assess via
859 modeling the rates that determines changes in mature mRNA levels.")
860 (license license:gpl2)))