Rscripts with config files to analyse/plot RNAseq data. Each R scripts which begins with 'step' can either be sourced from RStudio or launched in commandline mode: Rscript step.... Each of this script require a config file.
I suggest you to clone the whole repository to get access to all scripts and examples of config files.
A full documentation is available here
An example of analysis is available here where you can see examples of plots you can get.
If you have any issue/question/remark, feel free to open an issue in github or send me an email to lucille.delisle@epfl.ch