- Download and install the current version of the R Programming Language for your operating system
- Download and install the graphical user interface for R, called RStudio
- Download a ‘code aware’ text editor. I use Sublime, but also find Microsoft’s Visual Studio Code an excellent choice for working with scripts outside of RStudio.
- If you have a Mac, download the latest version of XCode developer tools
- If you have a PC, download Cygwin to give your system many linux-like capabilities
- Here are my instructions for installing Kallisto,the program we’ll use for mapping reads to transcripts. We will install this program together in class
- Download the Java-based program for running GSEA. This requires that you sign-up for a free account. You may also need to update to the latest version of Java for this application to run properly.
- Download the network analysis platform, Cytoscape
- If you have a PC, you will need to download RTools