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authorRicardo Wurmus <rekado@elephly.net>2023-03-30 14:10:45 +0200
committerRicardo Wurmus <rekado@elephly.net>2023-03-30 14:10:45 +0200
commit6d1cc311e59d876ed3712d2173762e34dcad1288 (patch)
treeb847d0ad30c093a3da457fbe0e0bfbb056bd13b0
parentde1c49c25de2d5e42a8e8074eaf632ad9959dbd6 (diff)
downloadguix-6d1cc311e59d876ed3712d2173762e34dcad1288.tar.gz
guix-6d1cc311e59d876ed3712d2173762e34dcad1288.zip
gnu: Add r-missmethyl.
* gnu/packages/bioconductor.scm (r-missmethyl): New variable.
-rw-r--r--gnu/packages/bioconductor.scm50
1 files changed, 50 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 85b1c050be..a91ee8fe06 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1674,6 +1674,56 @@ in Nature Genetics, January 2018.")
methylation arrays.")
(license license:artistic2.0)))
+(define-public r-missmethyl
+ (package
+ (name "r-missmethyl")
+ (version "1.32.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "missMethyl" version))
+ (sha256
+ (base32
+ "1rrm8m68kgjkrw1wdli5lrwqlavhbm490zgnj5vafzpvx7xajfma"))))
+ (properties `((upstream-name . "missMethyl")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-annotationdbi
+ r-biasedurn
+ r-biobase
+ r-biocgenerics
+ r-genomicranges
+ r-go-db
+ r-illuminahumanmethylation450kanno-ilmn12-hg19
+ r-illuminahumanmethylation450kmanifest
+ r-illuminahumanmethylationepicanno-ilm10b4-hg19
+ r-illuminahumanmethylationepicmanifest
+ r-iranges
+ r-limma
+ r-methylumi
+ r-minfi
+ r-org-hs-eg-db
+ r-ruv
+ r-s4vectors
+ r-statmod
+ r-stringr
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/missMethyl")
+ (synopsis "Analyzing Illumina HumanMethylation BeadChip data")
+ (description
+ "This is a package for normalization, testing for differential
+variability and differential methylation and gene set testing for data from
+Illumina's Infinium HumanMethylation arrays. The normalization procedure is
+subset-quantile within-array normalization (SWAN), which allows Infinium I and
+II type probes on a single array to be normalized together. The test for
+differential variability is based on an empirical Bayes version of Levene's
+test. Differential methylation testing is performed using RUV, which can
+adjust for systematic errors of unknown origin in high-dimensional data by
+using negative control probes. Gene ontology analysis is performed by taking
+into account the number of probes per gene on the array, as well as taking
+into account multi-gene associated probes.")
+ (license license:gpl2)))
+
(define-public r-msdata
(package
(name "r-msdata")