Software requirements

Everyone is expected to bring their own internet-enabled laptop equiped with either the recent Mac or Windows OS. All the software listed below is free and we will help you install each program during class.

Part I

  • 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

Part II

  • 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