This repository hosts the Python and R Jupyter notebooks used to perform the analyses described in the manuscript “Systematically Characterizing the Roles of E3-Ligase Family Members in Inflammatory Responses with Massively Parallel Perturb-seq” by Geiger-Schuller, Eraslan et al.

Analysis steps requiring visual inspection are implemented as Jupyter notebooks, while the remaining components are executed via command-line scripts for scalability and automation.

This pipeline includes the code for the following steps taken :

• Data QC and preprocessing
• Identification of the effects of perturbations on genes
• Learning the regulatory topology of perturbed and impacted genes
• Relating the regulatory (genetic) topology to physical interactions

File and Directory Structure

SRC/Pipeline/parameters.py file contains all the user defined parameters and input/output file names.