gnu: r-missmethyl: Move out of experiments section.
* gnu/packages/bioconductor.scm (r-missmethyl): Move from experiments section to packages section.
parent
e74e9f6240
commit
2edbfd43aa
|
@ -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")
|
||||
|
|
Reference in New Issue