The option to analyze RNA-Seq data using DESeq2 within Geneious is available in R10.1 and later. To do this on a Linux computer, 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. Note that Geneious 2023.1.1 or newer is required for DESeq2 integration.
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 4.3 or greater. For more information, or more detailed instructions for select Linux distributions, refer to the R Project website.
R installation on Ubuntu:
- On the terminal, enter the following commands to install R and its dependencies:
$ sudo apt-get update $ sudo apt-get install libcurl4-openssl-dev libxml2-dev libssl-dev $ sudo apt-get install r-base r-base-dev
- You can now proceed with Installing DESeq2 (below)
R installation on Centos or Red Hat Enterprise Linux:
- On the terminal, enter the following commands to install Rs dependencies:
$ sudo yum install curl $ sudo yum install libcurl libcurl-devel $ sudo yum install libxml2 libxml2-devel
- Now install R with the following command:
$ sudo yum install R
- You can now proceed with DESeq2 installation
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.
Download the R source archive from the R project website
On the terminal, go to the directory where you downloaded the the source
Extract the archive:
$ tar -xvzf R-4.3.Y.tar.gz
(Replace 4.3.Y with the version you are installing)
- Enter the source directory:
- Run the following commands to build and install R:
$ ./configure --prefix=$HOME/R $ ./configure --prefix=$HOME/R
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
You can add this directory to your PATH variable or run R from the terminal with the command
You can now proceed with DESeq2 installation.
Once you have installed R, you must install Bioconductor, then use Bioconductor to install DESeq2.
From the terminal, launch R normally using the command: R
- Install Bioconductor:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
- Install DESeq2:
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
- Quit R by entering
CTRL-D. You will be asked whether you'd like to save your workspace image; you may answer 'n' (answer 'y' if you'd like to use R from the terminal in the future and wish to save the history of the commands you used).
If you are on a version of R that does not install DESeq2 version 1.14.1 by default you may experience problems. You can install version 1.14.1 by performing the following steps:
- Download DESeq2 1.14.1 from https://www.bioconductor.org/packages/3.4/bioc/src/contrib/DESeq2_1.14.1.tar.gz to your computer, for example, /home/geneious/Downloads
- Run R
Remove any other installed DESeq2 versions with remove.packages("DESeq2").
Note: this will remove all installed DESeq2 versions
- To install DESeq2 1.14.1, type install.packages("/path/to/DESeq2") which in this example would be install.packages("/home/geneious/Downloads/DESeq2_1.14.1.tar.gz") and wait for the process to complete
- Once it has completed exit R. You should now be able to run DESeq2 from within Geneious using the R path you used in step 4.