Installation instructions

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 the 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
install.packages("BiocManager")

# non-Bioconductor packages installation
install.packages(
  c("openxlsx","gplots","ggplot2",
  "RColorBrewer","glmnet","factoextra",
  "FactoMineR","caret","survival","survminer"),
  repos="https://cloud.r-project.org"
)

# Bioconductor packages installation
BiocManager::install(
  c("Biobase","GEOquery","limma",
  "piano","mogene10sttranscriptcluster.db",
  "gProfileR", "gprofiler2", "clusterProfiler",
  "sva","genefilter","TCGAbiolinks","msigdbr",
  "edgeR","SummarizedExperiment","DO.db", "HDO.db",
  "hugene10sttranscriptcluster.db")
)

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
load_libraries<-function(){
  lr <- TRUE
  load_res<-suppressPackageStartupMessages(
    library("openxlsx",logical.return = lr) &
    library("gplots",logical.return = lr) &
    library("ggplot2",logical.return = lr) &
    library("RColorBrewer",logical.return = lr) &
    library("glmnet",logical.return = lr) &
    library("factoextra",logical.return = lr) &
    library("FactoMineR",logical.return = lr) &
    library("caret",logical.return = lr) &
    library("survival",logical.return = lr) &
    library("survminer",logical.return = lr) &
    library("Biobase",logical.return = lr) &
    library("GEOquery",logical.return = lr) &
    library("limma",logical.return = lr) &
    library("mogene10sttranscriptcluster.db",logical.return = lr) &
    library("gProfileR",logical.return = lr) &
    library("gprofiler2",logical.return = lr) &
    library("clusterProfiler",logical.return = lr) &
    library("sva",logical.return = lr) &
    library("genefilter",logical.return = lr) &
    library("TCGAbiolinks",logical.return = lr) &
    library("edgeR",logical.return = lr) &
    library("SummarizedExperiment",logical.return = lr) &
    library("piano",logical.return = lr) &
    library("msigdbr",logical.return = lr) &
    library("DO.db",logical.return = lr) &
    library("hugene10sttranscriptcluster.db",logical.return = lr)
  )
  if(load_res){
    message("Library installation and loading has finished successfully.")
  }else{
    message("An error occurred while installing or loading the libraries, please try again or ask for help.")
  }
}

load_libraries()

Contact

Contact the course team if you have any trouble with the installations. For this purpose, please use the provided discord channel:

• https://discord.gg/Rh9yZjWfP

Troubleshooting

If you have installed R previously, and don’t have the latest version (R 4.3.1) you might need to re-install all previously installed packages. To do this simply you can follow the instruction in this tutorial.

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