Bioconductor R/Extension

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Bioconductor is based on R and can therefore be extended with additional packages, that can be downloaded from the Bioconductor web site. For installing a package, you first need to start an interactive R session:

module load gcc/4.8.2 bioconductor/3.0
R

Afterwards you need to source the biocLite.R script:

source("http://bioconductor.org/biocLite.R")

As an example, we are installing the Bioconductor package a4:

biocLite("a4")

Since users do not have write permission in the Bioconductor installation directory, you will be asked if you would like to install the package locally:

Would you like to use a personal library instead?  (y/n) y
Would you like to create a personal library
~/R/x86_64-slackware-linux-gnu-library/3.1
to install packages into?  (y/n)

After confirming that you would like to go for a local installation, Bioconductor will download and install the package as well as its dependencies. At the end you will be asked if you would like to update some already installed packages for which there exist newer versions. Please reply with no, as your user does not have write permission in the installation directory.