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authorRicardo Wurmus <rekado@elephly.net>2019-12-18 15:23:27 +0100
committerRicardo Wurmus <rekado@elephly.net>2019-12-18 15:29:07 +0100
commitff1146b9b1ade0692c82cf0135790d7796134a99 (patch)
tree127e3d3eae710a62215cfa2656b04e5dcee0b1a4
parent6f15ea24158aac4c265bb0a93d199123dad9c02e (diff)
downloadguix-ff1146b9b1ade0692c82cf0135790d7796134a99.tar
guix-ff1146b9b1ade0692c82cf0135790d7796134a99.tar.gz
gnu: Add r-curatedtcgadata.
* gnu/packages/bioconductor.scm (r-curatedtcgadata): New variable.
-rw-r--r--gnu/packages/bioconductor.scm33
1 files changed, 33 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b9ee81a560..2ca1679f8b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -900,6 +900,39 @@ examples' of Affymetrix data, unlike the artificial examples included in the
package @code{affy}.")
(license license:gpl2+)))
+(define-public r-curatedtcgadata
+ (package
+ (name "r-curatedtcgadata")
+ (version "1.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
+ (sha256
+ (base32
+ "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
+ (properties
+ `((upstream-name . "curatedTCGAData")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationhub" ,r-annotationhub)
+ ("r-experimenthub" ,r-experimenthub)
+ ("r-hdf5array" ,r-hdf5array)
+ ("r-multiassayexperiment" ,r-multiassayexperiment)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://bioconductor.org/packages/curatedTCGAData/")
+ (synopsis "Curated data from The Cancer Genome Atlas")
+ (description
+ "This package provides publicly available data from The Cancer Genome
+Atlas (TCGA) as @code{MultiAssayExperiment} objects.
+@code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
+number, mutation, microRNA, protein, and others) with clinical / pathological
+data. It also links assay barcodes with patient identifiers, enabling
+harmonized subsetting of rows (features) and columns (patients / samples)
+across the entire multi-'omics experiment.")
+ (license license:artistic2.0)))
+
;;; Packages