shinyMethyl

Package	BioC-release	BioC-devel
shinyMethyl
shinyMethylData

Authors: Jean-Philippe Fortin and Kasper Daniel Hansen

Welcome to shinyMethyl, an interactive R application based on the shiny package for exploration of DNA methylation data from Illumina arrays (450k and EPIC arrays). shinyMethyl is part of the Bioconductor project.

The shinyMethyl paper can be found here

Installation

First, you will need to install at least the following packages from Bioconductor

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

and from CRAN

install.packages("httpuv")
install.packages("devtools")
install.packages("matrixStats")
install.packages("RColorBrewer")

To install the development version of shinyMethyl:

library(devtools)
install_github("rstudio/shiny")
install_github("jfortin1/shinyMethyl")
install_github("jfortin1/shinyMethylData")

Vignette

You can find the vignette for shinyMethyl at https://github.com/Jfortin1/shinyMethyl/blob/master/vignettes/shinyMethyl.pdf

Quick example

After installation, you can launch shinyMethyl with an example dataset from TCGA with the following code:

library(shinyMethyl)
library(shinyMethylData)
runShinyMethyl(summary.tcga.raw, summary.tcga.norm)

Citation

To cite package shinyMethyl in publications use:

Fortin J, Fertig EJ and Hansen KD (2014). “shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R.”, F1000Research

A BibTeX entry for LaTeX users is

@Article{shinymethyl, author = {Jean-Philippe Fortin and Elana J. Fertig and Kasper D. Hansen}, title = {{shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R}}, journal = {F1000Research}, year = {2014}, volume = {3}, pages = {175}, doi = {10.12688/f1000research.4680.2}, pubmed = {25285208} }