* gnu/packages/bioinformatics.scm (r-sva): New variable. --- gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm
b/gnu/packages/bioinformatics.scm
index d82b6c0..c6acab1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7995,3 +7995,38 @@ immunoprecipitation and target enrichment on small
gene panels. Thereby,
CopywriteR constitutes a widely applicable alternative to available copy
number detection tools.")
(license license:gpl2)))
+
+(define-public r-sva
+ (package
+ (name "r-sva")
+ (version "3.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "sva" version))
+ (sha265
+ (base32
+ "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-genefilter" ,r-genefilter)))
+ (home-page "http://bioconductor.org/packages/sva";)
+ (synopsis "Surrogate variable analysis")
+ (description
+ "This package contains functions for removing batch effects and
+other unwanted variation in high-throughput experiment. Specifically,
+the sva package contains functions for the identifying and building
+surrogate variables for high-dimensional data sets. Surrogate variables
+are covariates constructed directly from high-dimensional data (like gene
+expression/RNA sequencing/methylation/brain imaging data) that can be used
+in subsequent analyses to adjust for unknown, unmodeled, or latent sources
+of noise. The sva package can be used to remove artifacts in three ways:
+1. identifying and estimating surrogate variables for unknown sources of
+variation in high-throughput experiments Leek and Storey 2007 PLoS
Genetics,
+ 2008 PNAS,2. directly removing known batch effects using ComBat
+Johnson et al. 2007 Biostatistics and 3. removing batch effects with known
+control probes Leek 2014 biorXiv. Removing batch effects and using
surrogate
+variables in differential expression analysis have been shown to reduce
+dependence, stabilize error rate estimates, and improve reproducibility,
+see Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat.
Reviews Genetics.")
+ (license license:artistic2.0)))
--
1.9.1
0001-gnu-Add-r-sva.patch
Description: Binary data
