wateRmelon

DOI: 10.18129/B9.bioc.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 (3.15)

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

Author: Leo Schalkwyk <lschal at essex.ac.uk>, C Gorrie-Stone <lschal at essex.ac.uk>, Tyler Pidsley <lschal at essex.ac.uk>, J Wong <lschal at essex.ac.uk>, Ruth Touleimat <lschal at essex.ac.uk>, Chloe Defrance <lschal at essex.ac.uk>, CY Teschendorff <lschal at essex.ac.uk>, Nizar Maksimovic <lschal at essex.ac.uk>, Matthieu El Khoury <lschal at essex.ac.uk>, Andrew Wang <lschal at essex.ac.uk>, Jovana Schalkwyk <lschal at essex.ac.uk>, Louis Gorrie-Stone <lschal at essex.ac.uk>, Y Pidsley <lschal at essex.ac.uk>, Yucheng Wong <lschal at essex.ac.uk>

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

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

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("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

PDF   Reference Manual

Details

biocViews DNAMethylation, Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version 2.1.0
In Bioconductor since BioC 2.12 (R-3.0) (8.5 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
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/wateRmelon
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/wateRmelon
Package Short Url https://bioconductor.org/packages/wateRmelon/
Package Downloads Report Download Stats

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