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authorRicardo Wurmus <rekado@elephly.net>2019-03-29 22:18:49 +0100
committerRicardo Wurmus <rekado@elephly.net>2019-03-30 08:55:45 +0100
commite99380d67b459128807f27184b93f0b2a9e6c3fd (patch)
treea33ae2ed0716f624854ff4d001c25d9f1ad0b457 /gnu/packages/bioconductor.scm
parent303f2ed1c6447bd01e5310ea16aec6cbd0153a5b (diff)
downloadpatches-e99380d67b459128807f27184b93f0b2a9e6c3fd.tar
patches-e99380d67b459128807f27184b93f0b2a9e6c3fd.tar.gz
gnu: Add r-gcrma.
* gnu/packages/bioconductor.scm (r-gcrma): New variable.
Diffstat (limited to 'gnu/packages/bioconductor.scm')
-rw-r--r--gnu/packages/bioconductor.scm36
1 files changed, 36 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4c31ffcc0d..91a5a66ec2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3762,3 +3762,39 @@ functions to perform a signature analysis with known signatures and a
signature analysis on @dfn{stratified mutational catalogue} (SMC) are
provided.")
(license license:gpl3)))
+
+(define-public r-gcrma
+ (package
+ (name "r-gcrma")
+ (version "2.54.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "gcrma" version))
+ (sha256
+ (base32
+ "1v5fi98gdmj002ryq0rgsg2l4x3m3w5pz4h3bx4v8lk15azafgim"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affy" ,r-affy)
+ ("r-affyio" ,r-affyio)
+ ("r-biobase" ,r-biobase)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-biostrings" ,r-biostrings)
+ ("r-xvector" ,r-xvector)))
+ (home-page "https://bioconductor.org/packages/gcrma/")
+ (synopsis "Background adjustment using sequence information")
+ (description
+ "Gcrma adjusts for background intensities in Affymetrix array data which
+include optical noise and @dfn{non-specific binding} (NSB). The main function
+@code{gcrma} converts background adjusted probe intensities to expression
+measures using the same normalization and summarization methods as a
+@dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
+to estimate probe affinity to NSB. The sequence information is summarized in
+a more complex way than the simple GC content. Instead, the base types (A, T,
+G or C) at each position along the probe determine the affinity of each probe.
+The parameters of the position-specific base contributions to the probe
+affinity is estimated in an NSB experiment in which only NSB but no
+gene-specific bidning is expected.")
+ ;; Any version of the LGPL
+ (license license:lgpl2.1+)))