This package aims to make preparing GSEA 1 input files as easy as possible, by providing the following two methods:

# GUI by Shiny App

shiny::runApp(system.file('shiny/app.R', package = 'qGSEA'))

The app’s usage should be pretty straightforward 2, and there is a detailed guide with screenshots.

# command line in R

refer to make_gsea_input().

1. If you haven’t install GSEA yet, here is a brief guide.

• download “javaGSEA Java Jar file” under Software tab
• download gene set collections (.gmt file) you want to analyse under MSigDB tab (choose h.all.v6.1.symbols.gmt if you get confused.