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 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",
  "sva","genefilter","TCGAbiolinks","msigdbr", 
  "edgeR","SummarizedExperiment","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(){
  load_res<-suppressPackageStartupMessages(
    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)
  )
  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 in the installations. For this purpose, please use the provided discord channel:

• https://discord.gg/2VrZxBB

Installing IGV

You can find IGV for Linux, Mac or Windows here. Please use the download version (2.8.10) not the java web application, as the latter is slower and requires internet access. Please download IGV with Jave included so you don’t need to install Java separately.

Troubleshooting

If you have installed R previously, and you don’t have the latest version (R 4.0.3) you might need to re-install all previously installed packages (under versions 3.X.X). To do this simply you can follow the instruction in this tutorial.

For IGV, 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 to allow Java use more memory: 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.