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authorRicardo Wurmus <rekado@elephly.net>2023-07-19 15:06:03 +0200
committerRicardo Wurmus <rekado@elephly.net>2023-07-19 15:29:14 +0200
commit2edbfd43aab8ff3a99dee552974b7c0153568ca4 (patch)
tree7c247c78ef2b8be93988715e236c2173df5f2cef
parente74e9f62405e6ff20f2a23c2c6c64c7007c52b9e (diff)
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gnu: r-missmethyl: Move out of experiments section.
* gnu/packages/bioconductor.scm (r-missmethyl): Move from experiments section to packages section.
-rw-r--r--gnu/packages/bioconductor.scm100
1 files changed, 50 insertions, 50 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b19daa2e3f..f2aecc2fd5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1731,56 +1731,6 @@ in Nature Genetics, January 2018.")
methylation arrays.")
(license license:artistic2.0)))
-(define-public r-missmethyl
- (package
- (name "r-missmethyl")
- (version "1.34.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "missMethyl" version))
- (sha256
- (base32
- "1jvrdr57mv93pcbyazcg1bcx1zd0kp72hi1if839gw54hk3igs3h"))))
- (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")
@@ -12850,6 +12800,56 @@ model.")
methylation arrays.")
(license license:artistic2.0)))
+(define-public r-missmethyl
+ (package
+ (name "r-missmethyl")
+ (version "1.34.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "missMethyl" version))
+ (sha256
+ (base32
+ "1jvrdr57mv93pcbyazcg1bcx1zd0kp72hi1if839gw54hk3igs3h"))))
+ (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-methylumi
(package
(name "r-methylumi")