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A benchmark of algorithms for the analysis of pooled CRISPR screens.

ABSTRACT: Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze CRISPR-pooled screens. Here, we provide a review of the commonly used algorithms in the computational analysis of pooled CRISPR screens. We develop a comprehensive simulation framework to benchmark and compare the performance of these algorithms using both synthetic and real datasets. Our findings inform parameter choices of CRISPR screens and provide guidance to researchers on the design and analysis of pooled CRISPR screens.

SUBMITTER: Bodapati S

PROVIDER: S-EPMC7063732 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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A benchmark of algorithms for the analysis of pooled CRISPR screens.

Bodapati Sunil S Daley Timothy P TP Lin Xueqiu X Zou James J Qi Lei S LS

Genome biology 20200309 1

Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze CRISPR-pooled screens. Here, we provide a review of the commonly used algorithms in the computational analysis of pooled CRISPR screens. We develop a comprehensive simulation framework to benchmark and compare the performance of these algorithms using both ...[more]

PMID: 32151271

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