Installation instructions

For this course you are expected to use two main softwares: RStudio, an Integrated Development Environment (IDE) for R, and the Integrative Genomics Viewer (IGV) that we use to visualise reads and coverage aligned on a reference genome.

Installing R Studio

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 at your console. This operation will take a few minutes.

# 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
source("https://bioconductor.org/biocLite.R")
biocLite(
  c("Biobase","GEOquery","limma","piano",
  "mogene10sttranscriptcluster.db","gProfileR","sva",
  "genefilter","TCGAbiolinks","edgeR","SummarizedExperiment")
)

 

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

Installing IGV

1. You are required to have Java 8 installed in your computer. In case you don’t have java, you can find it here.

2. After that is done, you can find IGV here. Please use the download version (not the java web start), as the latter is slower and require internet access.

NOTE: to run IGV on the Microsoft Windows operating system you will need to go to the directory to 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 in the installations.