Each participant must bring their own laptop (with a power supply or a really big battery) with a recent operating system version (either Mac or Windows). Before the first class, please attempt to complete Parts I and II of the following steps (you can safely leave part III for later). If you run into problems with any of these tasks please email Wade or Matei or Herb, or use the “Contact Us” form in the main menu above. All software listed below is free and open-source.
Part I
Get your R environment set up:
- Download and install the appropriate version of the R Programming Language for your operating system
- Download and install the IDE for R, called RStudio
- Install Bioconductor
- Install Bioconductor packages flowCore, flowViz, flowStats and flowFP (hint: the bioconductor website tells you how to use BiocManager to do this)
NOTE: Some packages require a compiler for installation. If you run into that problem please consult Part III below.
Part II
Get your git set up:
- Dowload and install Git
* On a Windows machine, first install Git, followed by GitHub Desktop
* On a Mac, just install Git - Create an account on Github (I’ll share my code with you via Github, and later you’ll be able to share your code with the world or any part thereof)
Part III
Get tools to compile and build packages (advanced). Some packages (notably FlowSOM) may require compilers to build from source.
- if you have a Windows machine, you’ll need RTools to build packages.
- If you’re on a Mac, follow these instructions.