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12/16: gnu: Add r-missmethyl.
From: |
guix-commits |
Subject: |
12/16: gnu: Add r-missmethyl. |
Date: |
Thu, 30 Mar 2023 08:28:05 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit 6d1cc311e59d876ed3712d2173762e34dcad1288
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Thu Mar 30 14:10:45 2023 +0200
gnu: Add r-missmethyl.
* gnu/packages/bioconductor.scm (r-missmethyl): New variable.
---
gnu/packages/bioconductor.scm | 50 +++++++++++++++++++++++++++++++++++++++++++
1 file changed, 50 insertions(+)
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")
- 03/16: gnu: Add r-jade., (continued)
- 03/16: gnu: Add r-jade., guix-commits, 2023/03/30
- 04/16: gnu: Add r-isva., guix-commits, 2023/03/30
- 06/16: gnu: Add r-globaltest., guix-commits, 2023/03/30
- 08/16: gnu: Add r-champdata., guix-commits, 2023/03/30
- 09/16: gnu: Add r-ruv., guix-commits, 2023/03/30
- 10/16: gnu: Add r-illumina450probevariants-db., guix-commits, 2023/03/30
- 01/16: gnu: Add r-illuminahumanmethylation450kmanifest., guix-commits, 2023/03/30
- 13/16: gnu: Add r-dss., guix-commits, 2023/03/30
- 14/16: gnu: Add r-dmrcate., guix-commits, 2023/03/30
- 16/16: gnu: Add r-champ., guix-commits, 2023/03/30
- 12/16: gnu: Add r-missmethyl.,
guix-commits <=
- 11/16: gnu: Add r-illuminahumanmethylationepicanno-ilm10b4-hg19., guix-commits, 2023/03/30