MethylAid

DOI: 10.18129/B9.bioc.MethylAid    

Visual and interactive quality control of large Illumina DNA Methylation array data sets

Bioconductor version: Release (3.11)

A visual and interactive web application using RStudio's shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.

Author: Maarten van Iterson [aut, cre], Elmar Tobi[ctb], Roderick Slieker[ctb], Wouter den Hollander[ctb], Rene Luijk[ctb] and Bas Heijmans[ctb]

Maintainer: L.J.Sinke <L.J.Sinke at lumc.nl>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("MethylAid")

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("MethylAid")

 

PDF	R Script	MethylAid: Visual and Interactive quality control of Illumina Human DNA Methylation array data
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, DNAMethylation, GUI, MethylationArray, Microarray, QualityControl, Software, TwoChannel, Visualization
Version	1.22.0
In Bioconductor since	BioC 3.0 (R-3.1) (6 years)
License	GPL (>= 2)
Depends	R (>= 3.4)
Imports	Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi(>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils
LinkingTo
Suggests	BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit
SystemRequirements
Enhances
URL
Depends On Me	MethylAidData
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MethylAid_1.22.0.tar.gz
Windows Binary	MethylAid_1.22.0.zip
macOS 10.13 (High Sierra)	MethylAid_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MethylAid
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MethylAid
Package Short Url	https://bioconductor.org/packages/MethylAid/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive