To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MethylAid")

In most cases, you don't need to download the package archive at all.

MethylAid

 

   

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

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

Bioconductor version: Development (3.4)

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: M. van Iterson <mviterson at gmail.com>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MethylAid")

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 1.7.2
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License GPL (>= 2)
Depends R (>= 3.0)
Imports Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi(>= 1.17.9), methods, RColorBrewer, shiny, stats, utils
LinkingTo
Suggests BiocStyle, knitr, MethylAidData, minfiData, RUnit
SystemRequirements
Enhances
URL https://github.com/mvaniterson/methylaid
BugReports https://github.com/mvaniterson/methylaid/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source MethylAid_1.7.2.tar.gz
Windows Binary MethylAid_1.7.2.zip
Mac OS X 10.9 (Mavericks) MethylAid_1.7.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/MethylAid
Package Short Url http://bioconductor.org/packages/MethylAid/
Package Downloads Report Download Stats

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