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MethylAid

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


Bioconductor version: Release (3.18)

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>

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

Installation

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


if (!require("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")
MethylAid: Visual and Interactive quality control of Illumina Human DNA Methylation array data PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, DNAMethylation, GUI, MethylationArray, Microarray, QualityControl, Software, TwoChannel, Visualization
Version 1.36.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 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
System Requirements
URL
See More
Suggests BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit
Linking To
Enhances
Depends On Me MethylAidData
Imports Me
Suggests Me
Links To Me
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Package Archives

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

Source Package MethylAid_1.36.0.tar.gz
Windows Binary MethylAid_1.36.0.zip
macOS Binary (x86_64) MethylAid_1.36.0.tgz
macOS Binary (arm64) MethylAid_1.36.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MethylAid
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MethylAid
Bioc Package Browser https://code.bioconductor.org/browse/MethylAid/
Package Short Url https://bioconductor.org/packages/MethylAid/
Package Downloads Report Download Stats