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.

    • go to official download
    • 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.
  2. You just need to click anywhere you like and it would show useful hint.↩︎