This repository contains code to reproduce the synthetic lethality analysis performed in "Caspase 3 and caspase 7 promote adaptation to non-lethal stress and their dual loss phenocopies PARP1 inhibition" Gayathri Samarasekera; Nancy E Go; Courtney Choutka; Jing Xu; Yuka Takemon; Jennifer Chan; Michelle Chan; Shivani Perera; Samuel Aparicio; Gregg B Morin; Marco A Marra; Suganthi Chittaranjan; Sharon M Gorski. PLOS Biology. 2025. https://doi.org/10.1371/journal.pbio.3003034
Please note, GRETTA v1.0.0 (https://github.com/MarraLab/GRETTA) was used for this project. Some functionalities described here are now integrated into the latest version of GRETTA v2.4.0.
There are dependencies in these scripts. Please first run script 1..., then script 2..., and then script 3....