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 directly want to start your analysis go here.
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