Differential expression analysis with DESeq2

(Mike Love and Rob Patro)

Upgrade R to the very latest (3.4.x)

sudo echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" | sudo tee -a /etc/apt/sources.list
gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --export E084DAB9 | sudo apt-key add -

sudo apt-get update && sudo apt-get install -y r-base r-base-dev gdebi-core

Make sure you’re running RStudio

For this, we will again be working exclusively in RStudio! Try to connect to a running RStudio Web server instance – you can get the Web address by running this command:

echo My RStudio Web server is running at: http://$(hostname):8787/

Install RStudio Web server

If you cannot connect, you’ll need to install it:

wget https://download2.rstudio.org/rstudio-server-1.0.143-amd64.deb
sudo gdebi -n rstudio-server-1.0.143-amd64.deb

And, finally, change the password to something you can remember:

sudo passwd tx160085

Install the DESeq2 prereqs

sudo apt-get install -y libxml2 libxml2-dev libcurl4-gnutls-dev libssl-dev

and then install DESeq2:

curl -O -L https://github.com/ngs-docs/angus/raw/2017/_static/install-deseq2.R

sudo Rscript --no-save install-deseq2.R


From this point on, we will be using the lesson from Mike Love’s asthma repository. To get a copy of it, execute:

git clone https://github.com/mikelove/asthma

and then open asthma/scripts/asthma.Rmd in RStudio.