Introduction to qGSEA

Zhuoer Dong

2022-05-04

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().

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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.↩︎