Installation instructions

For this course, you are expected to use (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

# non-Bioconductor packages installation

# Bioconductor packages installation

NB: If you use Linux, you might have to install some system packages before you can successfully install the R packages listed below. For example, you can run the following command in Ubuntu to install most, if not all, of the required system dependencies:

sudo apt install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev

Finally, whatever your Operating System, you can test if the installation worked by copy-pasting the following commands to the RStudio console.

# test if install worked
    library("openxlsx",logical.return = T) &
    library("gplots",logical.return = T) &
    library("ggplot2",logical.return = T) &
    library("RColorBrewer",logical.return = T) &
    library("glmnet",logical.return = T) &
    library("factoextra",logical.return = T) &
    library("FactoMineR",logical.return = T) &
    library("caret",logical.return = T) &
    library("survival",logical.return = T) &
    library("survminer",logical.return = T) &
    library("Biobase",logical.return = T) &
    library("GEOquery",logical.return = T) &
    library("limma",logical.return = T) &
    library("mogene10sttranscriptcluster.db",logical.return = T) &
    library("gProfileR",logical.return = T) &
    library("sva",logical.return = T) &
    library("genefilter",logical.return = T) &
    library("TCGAbiolinks",logical.return = T) &
    library("edgeR",logical.return = T) &
    library("SummarizedExperiment",logical.return = T) &
    library("piano",logical.return = T)
    message("Library installation and loading has finished successfully.")
    message("An error occurred while installing or loading the libraries, please try again or ask for help.")


Contact the course team if you have any trouble in the installations.

Contact the course team if you have any trouble with these instructions.