See individual subfolders for instructions how to use the code.

All of the code can be run on an unix/OSX computer. The software dependencies are tracked via docker or conda. Installation of dependencies should take about an hour on a typical laptop. Code was developed and tested on Mac OSX Big Sur (11.6).

All analyses except the ChIP-seq integration one take approximately an hour to complete on a normal computer. The ChIP-seq integration pipeline was designed to run on a computer cluster with SLURM installed and takes about a day to complete.

For more details, see README files inside the subfolders.