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wateRmelon

This is the development version of wateRmelon; for the stable release version, see wateRmelon.

Illumina 450 and EPIC methylation array normalization and metrics

Bioconductor version: Development (3.18)

15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.

Author: Leo C Schalkwyk [cre, aut], Tyler J Gorrie-Stone [aut], Ruth Pidsley [aut], Chloe CY Wong [aut], Nizar Touleimat [ctb], Matthieu Defrance [ctb], Andrew Teschendorff [ctb], Jovana Maksimovic [ctb], Louis Y El Khoury [ctb], Yucheng Wang [ctb]

Maintainer: Leo C Schalkwyk <lschal at essex.ac.uk>

Citation (from within R, enter citation("wateRmelon")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("wateRmelon")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("wateRmelon")
wateRmelon User's Guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DNAMethylation, Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version 2.7.0
In Bioconductor since BioC 2.12 (R-3.0) (10.5 years)
License GPL-3
Depends R (>= 3.5.0), Biobase, limma, methods, matrixStats, methylumi, lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19, illuminaio
Imports Biobase
Linking To
Suggests RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BiocStyle, knitr, rmarkdown, IlluminaHumanMethylationEPICmanifest, irlba, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore
System Requirements
Enhances minfi
URL
See More
Depends On Me bigmelon, skewr
Imports Me ChAMP, MEAT
Suggests Me RnBeads
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package wateRmelon_2.7.0.tar.gz
Windows Binary wateRmelon_2.7.0.zip
macOS Binary (x86_64) wateRmelon_2.7.0.tgz
macOS Binary (arm64) wateRmelon_2.7.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/wateRmelon
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/wateRmelon
Bioc Package Browser https://code.bioconductor.org/browse/wateRmelon/
Package Short Url https://bioconductor.org/packages/wateRmelon/
Package Downloads Report Download Stats