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"))
You can find IGV for Linux, Mac or Windows here. Please use the download version 2.8.10 (not the IGV web application), as the latter is slower and requires internet access. Note, we highly recommend using the IGV with Java included.
If it crashes when you open it, or when you load a file, and you are using the Microsoft Windows operating system, follow these instructions: go to the directory where you downloaded IGV, “right-click” the file “igv.bat”, click on “Edit” (it should open “Notepad”) and in the text, where it says “-Xmx4g”, change it so “-Xmx1g”. Save the file and exit the editor. You should now be able to run IGV by double-clicking the “igv.bat” file.
Contact the course team if you have any trouble with these instructions.