GRETTA: an R package for mapping in silico genetic interaction and essentiality networks.

Abstract

Mapping genetic interactions and essentiality networks in human cell lines has been used to identify vulnerabilities of cells carrying specific genetic alterations and to associate novel functions to genes, respectively. In vitro and in vivo genetic screens to decipher these networks are resource-intensive, limiting the throughput of samples that can be analyzed. In this application note, we provide an R package we call Genetic inteRaction and EssenTiality neTwork mApper (GRETTA). GRETTA is an accessible tool for in silico genetic interaction screens and essentiality network analyses using publicly available data, requiring only basic R programming knowledge. The R package, GRETTA, is licensed under GNU General Public License v3.0 and freely available at https://github.com/ytakemon/GRETTA and https://doi.org/10.5281/zenodo.6940757, with documentation and tutorial. A Singularity container is also available at https://cloud.sylabs.io/library/ytakemon/gretta/gretta.