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bioRxiv · 10.1101/2022.09.21.508787

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

Takemon, Y.·Marra, M. A.
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Abstract

SummaryMapping genetic interaction and essentiality networks in human cell lines have 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 mApper (GRETA). GRETA is an accessible tool for in silico genetic interaction screens and essentiality network analyses using publicly available data, requiring only basic R programming knowledge. Availability and implementationThe R package, GRETA, is licensed under GNU General Public License v3.0 and freely available at https://github.com/ytakemon/GRETA 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/greta/greta. Contactmmarra@bcgsc.ca Supplemental informationSupplemental materials are available at Bioinformatics online. Issue sectionSystems biology

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Takemon, Y., Marra, M. A.. 2022-09-22. GRETA: an R package for mapping in silico genetic interaction and essentiality networks. https://doi.org/10.1101/2022.09.21.508787

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