Before you can analyze RNA-Seq data using DESeq2 within Geneious on Linux, you will ﬁrst need to install R and the DESeq2 package, following the instructions below. This is only necessary for Linux systems, as Geneious will automatically install R on Windows and MacOS systems the ﬁrst time DESeq2 is run.
Once R has been installed, you will be able to run the DESeq2 method to Compare Expression Levels within Geneious like any other Geneious operation. You may need to specify the R executable location in the DESeq2 options, for example, if R is not installed on PATH.
Note that the installation instructions for R on Ubuntu, Centos or Red Hat Enterprise Linux require sudo or root access. If you do not have root access, you can install R from source in your home directory.
Install R version 3.3.0 or greater. For more information, or more detailed instructions for select Linux distributions, refer to the R Project website.
R installation on Ubuntu:
R installation on Centos or Red Hat Enterprise Linux:
R installation from source in your home directory
You should only install R from source in your home directory if you do not have root access.
(Replace 3.X.Y with the version you are installing)
Note that if the ﬁrst command fails because of missing libraries, it may still be possible to install these dependencies without root access.
This will install R in your home directory under $HOME/R/bin.
You can add this directory to your PATH variable or run R from the terminal with the command ~/R/bin/R.
You can now proceed with DESeq2 installation.
Once you have installed R, you must install Bioconductor, then use Bioconductor to install DESeq2. Only DESeq2 version 1.14.1 is currently supported.
Note that you will be asked to install any dependent packages that are not already installed. This step can take some time: wait for it to ﬁnish before proceeding