For this course, you are expected to use R (a programming language and environment for statistical computing and graphics) and RStudio (an Integrated Development Environment (IDE) for R).
Installing R and RStudio
1. The first step is to install R software. We recommend using pre-compiled versions provided here.
2. Next, you need to install RStudio, which provides a nice graphical interface for R. You can install the latest RStudio release here.
3. Install all the R libraries necessary for this course using RStudio. For this, open your RStudio and copy-paste the following code to your RStudio console. This operation will take a few minutes.
# install Bioconductor package manager
# Bioconductor packages installation
BiocManager::install(c("limma", "RColorBrewer", "sva", "Biobase", "GEOquery", "gplots", "gProfileR", "mgcv", "genefilter"))
Contact the course team if you have any trouble with these instructions.