1) Install latest version of R which can be downloaded from http://probability.ca/cran/.

2) Download and install the most recent version of R Studio desktop. If prompted to install git, select yes.

3) Install the BioConductor core packages. If you have installed R version 3.5.0 or higher, open R and at the ‘>’ prompt, paste the commands:

install.packages("BiocManager");
library(BiocManager);
BiocManager::install();

4) Install Java. The visualization program that we will be using (IGV) requires Java version 11. First check if you have it installed (instructions). Install Java 11 if needed.

5) Install the Integrative Genomics Viewer 2.8.3 (IGV). Follow the IGV Install Instructions for your operating system.

6) Install an SSH client if needed. Mac users already have a command line ssh program that can be run from the terminal. For Windows users, please download PuTTY.

7) Install the Loupe browser. First go to the 10x download pages. Enter your info and selectthe Loupe Browser 4.0.0 download for your operating system.

8) Download all example scRNA files for a loupe demonstration from our course server.