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](https://bioconductor.org/packages/release/bioc/html/methylGSA.html). The Bioconductor package vignette can be found [here](https://bioconductor.org/packages/release/bioc/vignettes/methylGSA/inst/doc/methylGSA-vignette.html). The `methylGSA` paper can be found [here](https://doi.org/10.1093/bioinformatics/bty892). Shiny app installation ------------ The following packages are required to be installed before launching the app. Packages from CRAN: ```{r} install.packages("DT") install.packages("ggplot2") install.packages("shinycssloaders") ``` Packages from Bioconductor: If analyzing 450K array, `IlluminaHumanMethylation450kanno.ilmn12.hg19` needs to be installed. ```{r} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("IlluminaHumanMethylation450kanno.ilmn12.hg19") ``` If analyzing EPIC array, `IlluminaHumanMethylationEPICanno.ilm10b4.hg19` needs to be installed. ```{r} 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: ```{r} library(methylGSA) methylGSA::runExample() ``` Step-by-step instructions ------------ A step-by-step instructions on the workflow of the app can be found [here](https://github.com/reese3928/methylGO-RShiny-app/raw/master/instructions.pdf). 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} }