summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorRicardo Wurmus <rekado@elephly.net>2019-09-15 22:41:03 +0200
committerRicardo Wurmus <rekado@elephly.net>2019-09-15 22:41:03 +0200
commitdf8576e5c93e765fc4f75c47698342b1f7aa9642 (patch)
tree7ac2dd7f44a3dfb539a9f6fe46d76a685490562a
parentfc3719cc0f91644b56e7572a81669398b5fd1c8d (diff)
downloadpatches-df8576e5c93e765fc4f75c47698342b1f7aa9642.tar
patches-df8576e5c93e765fc4f75c47698342b1f7aa9642.tar.gz
gnu: Add r-variantfiltering.
* gnu/packages/bioconductor.scm (r-variantfiltering): New variable.
-rw-r--r--gnu/packages/bioconductor.scm47
1 files changed, 47 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9fce21dc00..4f2d97025a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5838,3 +5838,50 @@ course data which includes dimensionality reduction, clustering, two-sample
differential expression testing and gene ranking techniques. The package also
provides methods for retrieving enriched pathways.")
(license license:lgpl3+)))
+
+(define-public r-variantfiltering
+ (package
+ (name "r-variantfiltering")
+ (version "1.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "VariantFiltering" version))
+ (sha256
+ (base32
+ "0vpghxacqcbaxx2scb5gfhcmfpw1lkls7h6qnbwbnmjwy01q2p17"))))
+ (properties
+ `((upstream-name . "VariantFiltering")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-dt" ,r-dt)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-genomicscores" ,r-genomicscores)
+ ("r-graph" ,r-graph)
+ ("r-gviz" ,r-gviz)
+ ("r-iranges" ,r-iranges)
+ ("r-rbgl" ,r-rbgl)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-shiny" ,r-shiny)
+ ("r-shinyjs" ,r-shinyjs)
+ ("r-shinythemes" ,r-shinythemes)
+ ("r-shinytree" ,r-shinytree)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)
+ ("r-xvector" ,r-xvector)))
+ (home-page "https://github.com/rcastelo/VariantFiltering")
+ (synopsis "Filtering of coding and non-coding genetic variants")
+ (description
+ "Filter genetic variants using different criteria such as inheritance
+model, amino acid change consequence, minor allele frequencies across human
+populations, splice site strength, conservation, etc.")
+ (license license:artistic2.0)))