In dongzhuoer/qGSEA: Simplest tool to prepare GSEA input files

knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

This package aims to make preparing GSEA ^install 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 ^[You just need to click anywhere you like and it would show useful hint.], and there is a detailed guide with screenshots.

command line in R

refer to make_gsea_input().

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

- go to [official download](http://software.broadinstitute.org/gsea/downloads.jsp)
- 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.