In this repository all code regarding the epigenetic drug screening on the K562 CRISPR-Cas9 DSB clone#5 with 19 integrations is uploaded.
In short we tested 162 epigenetic drugs for their effect on Cas9 cutting efficiency and DNA repair pathway balance.
All relevant processed files can be found here: zenodo.org and in the files_scripts folder.
Script #1: Parsing QC
General quality checks of the sequencing data. Includes read counts and viability check.
Scripts #2: Preprocessing drug screen and validations
Mutating sequencing data to large data frame. Adding all relevant annotations.
Script #3: Synergy calculations
Scripts related to the calculation of the chromatin context dependencies.
Scripts #4: Statistics & Plotting
All the plots are generated with these scripts, split up by figure.
