wateRmelon

DOI: 10.18129/B9.bioc.wateRmelon  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see wateRmelon.

Illumina 450 and EPIC methylation array normalization and metrics

Bioconductor version: 3.17

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>

Installation

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

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

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")

 

HTML	R Script	wateRmelon User's Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version	2.6.0
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
LinkingTo
Suggests	RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BiocStyle, knitr, rmarkdown, IlluminaHumanMethylationEPICmanifest, irlba, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore
SystemRequirements
Enhances	minfi
URL
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_2.6.0.tar.gz
Windows Binary	wateRmelon_2.6.0.zip (64-bit only)
macOS Binary (x86_64)	wateRmelon_2.6.0.tgz
macOS Binary (arm64)	wateRmelon_2.6.0.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