gnu: Add r-gcrma.

* gnu/packages/bioconductor.scm (r-gcrma): New variable.
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Ricardo Wurmus 2019-03-29 22:18:49 +01:00
parent 303f2ed1c6
commit e99380d67b
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@ -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+)))