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authorRicardo Wurmus <rekado@elephly.net>2019-03-29 22:42:19 +0100
committerRicardo Wurmus <rekado@elephly.net>2019-03-30 08:55:46 +0100
commit50d91770513bb52bd693080661758d8fd6aab89f (patch)
tree5c4ec4ee81ec49a295f638f9975a94b65c6b2d11
parenta6e1eb1a96799212815eda7b0408d778b7000022 (diff)
downloadpatches-50d91770513bb52bd693080661758d8fd6aab89f.tar
patches-50d91770513bb52bd693080661758d8fd6aab89f.tar.gz
gnu: Add r-xbseq.
* gnu/packages/bioconductor.scm (r-xbseq): New variable.
-rw-r--r--gnu/packages/bioconductor.scm37
1 files changed, 37 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d87d9135ff..c276f000b6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3943,3 +3943,40 @@ large RNA-seq experiments.")
sites, comparing two biological conditions, starting from known alternative
sites and alignments obtained from standard RNA-seq experiments.")
(license license:gpl3)))
+
+(define-public r-xbseq
+ (package
+ (name "r-xbseq")
+ (version "1.14.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "XBSeq" version))
+ (sha256
+ (base32
+ "0na0jiqfy40bzl243gqc2214k4hibv6v4ndiqwq0c5f78cyr6lph"))))
+ (properties `((upstream-name . "XBSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-deseq2" ,r-deseq2)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-locfit" ,r-locfit)
+ ("r-magrittr" ,r-magrittr)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-pracma" ,r-pracma)
+ ("r-roar" ,r-roar)))
+ (home-page "https://github.com/Liuy12/XBSeq")
+ (synopsis "Test for differential expression for RNA-seq data")
+ (description
+ "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
+expression} (DE), where a statistical model was established based on the
+assumption that observed signals are the convolution of true expression
+signals and sequencing noises. The mapped reads in non-exonic regions are
+considered as sequencing noises, which follows a Poisson distribution. Given
+measurable observed signal and background noise from RNA-seq data, true
+expression signals, assuming governed by the negative binomial distribution,
+can be delineated and thus the accurate detection of differential expressed
+genes.")
+ (license license:gpl3+)))