methylGSA

methylGSA is a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing.

The Bioconductor package can be found here.
The Bioconductor package vignette can be found here.
The methylGSA paper can be found here.

Shiny app installation

The following packages are required to be installed before launching the app.
Packages from CRAN:

install.packages("DT")    
install.packages("ggplot2")       
install.packages("shinycssloaders")     

Packages from Bioconductor:
If analyzing 450K array, IlluminaHumanMethylation450kanno.ilmn12.hg19 needs to be installed.

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("IlluminaHumanMethylation450kanno.ilmn12.hg19")

If analyzing EPIC array, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 needs to be installed.

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("IlluminaHumanMethylationEPICanno.ilm10b4.hg19")

Launch the app

After installation, the app can be launched with the following code:

library(methylGSA)
methylGSA::runExample()

Step-by-step instructions

A step-by-step instructions on the workflow of the app can be found here.

Citation

Ren, X., & Kuan, P. F. (2019). methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing. Bioinformatics, 35(11), 1958-1959.

@article{ren2019methylgsa,
title={methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing},
author={Ren, Xu and Kuan, Pei Fen},
journal={Bioinformatics},
volume={35},
number={11},
pages={1958--1959},
year={2019},
publisher={Oxford University Press}
}