GRETTA: an R package for mapping in silico genetic interaction and essentiality networks.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 37326978.
- Also identified by DOI 10.1093/bioinformatics/btad381 and PMC identifier 10284671.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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.
Medical subject headings
- Software