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authorRicardo Wurmus <rekado@elephly.net>2019-03-29 15:40:22 +0100
committerRicardo Wurmus <rekado@elephly.net>2019-03-29 17:13:45 +0100
commit32e0f906d775679d8b4e770d267d29cb77724360 (patch)
tree5b9d1068e9f6ddb6a04f48c200f76182c646197b /gnu
parente5bff3079d673d1d7816b0c30142935ef1e05791 (diff)
downloadpatches-32e0f906d775679d8b4e770d267d29cb77724360.tar
patches-32e0f906d775679d8b4e770d267d29cb77724360.tar.gz
gnu: Add r-atacseqqc.
* gnu/packages/bioconductor.scm (r-atacseqqc): New variable.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioconductor.scm44
1 files changed, 44 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0daea685e5..4ee14a4c08 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3302,3 +3302,47 @@ type and symbol colors.")
"This package provides infrastructure to store and access genome-wide
position-specific scores within R and Bioconductor.")
(license license:artistic2.0)))
+
+(define-public r-atacseqqc
+ (package
+ (name "r-atacseqqc")
+ (version "1.6.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ATACseqQC" version))
+ (sha256
+ (base32
+ "1rblvqar11fib6ip2hq0756vqi6qmncf90jw6i5p5lrgzmaxy8hn"))))
+ (properties `((upstream-name . "ATACseqQC")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-chippeakanno" ,r-chippeakanno)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-genomicscores" ,r-genomicscores)
+ ("r-iranges" ,r-iranges)
+ ("r-kernsmooth" ,r-kernsmooth)
+ ("r-limma" ,r-limma)
+ ("r-motifstack" ,r-motifstack)
+ ("r-preseqr" ,r-preseqr)
+ ("r-randomforest" ,r-randomforest)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/ATACseqQC/")
+ (synopsis "ATAC-seq quality control")
+ (description
+ "ATAC-seq, an assay for Transposase-Accessible Chromatin using
+sequencing, is a rapid and sensitive method for chromatin accessibility
+analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
+and DNAse-seq. The ATACseqQC package was developed to help users to quickly
+assess whether their ATAC-seq experiment is successful. It includes
+diagnostic plots of fragment size distribution, proportion of mitochondria
+reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
+footprints.")
+ (license license:gpl2+)))