GEMINI: a variational Bayesian approach to identify genetic interactions from combinatorial CRISPR screens

Systems for CRISPR-based combinatorial perturbation of two or more genes are emerging as powerful tools for uncovering genetic interactions. However, systematic identification of these relationships is complicated by sample, reagent, and biological variability. We develop a variational Bayes approac...

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Detalles Bibliográficos
Autores principales: Zamanighomi, Mahdi, Jain, Sidharth S., Ito, Takahiro, Pal, Debjani, Daley, Timothy P., Sellers, William R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6624979/
https://www.ncbi.nlm.nih.gov/pubmed/31300006
http://dx.doi.org/10.1186/s13059-019-1745-9
Descripción
Sumario:Systems for CRISPR-based combinatorial perturbation of two or more genes are emerging as powerful tools for uncovering genetic interactions. However, systematic identification of these relationships is complicated by sample, reagent, and biological variability. We develop a variational Bayes approach (GEMINI) that jointly analyzes all samples and reagents to identify genetic interactions in pairwise knockout screens. The improved accuracy and scalability of GEMINI enables the systematic analysis of combinatorial CRISPR knockout screens, regardless of design and dimension. GEMINI is available as an open source R package on GitHub at https://github.com/sellerslab/gemini. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1745-9) contains supplementary material, which is available to authorized users.