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

Genome Biology
Sunil BodapatiLei S Qi

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.

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Citations

Sep 17, 2020·PLoS Computational Biology·Patrick C FiauxGraham McVicker
Jun 11, 2020·International Journal of Molecular Sciences·Annamaria SalvatiGiorgio Giurato
Aug 23, 2020·Genes·Roberto SpreaficoAmalio Telenti
Jan 6, 2021·Current Opinion in Plant Biology·Changtian PanYiping Qi
Apr 4, 2021·Cancers·Laia Castells-RocaJordi Surrallés
Apr 10, 2021·Essays in Biochemistry·Chi Wai YipJay W Shin
May 23, 2021·The Journal of General Virology·Chloe E JonesDavid J Hughes
Sep 2, 2021·Cell Reports·Weizhong ChenQuanjiang Ji
Jun 25, 2021·Diabetes·Peng Yi, Noelle Morrow
Sep 18, 2021·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Carlos Pulido-Quetglas, Rory Johnson

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Methods Mentioned

BETA
fluorescence-activated cell sorting
RNA-seq
RSA
sgRNA knockout

Software Mentioned

RRA
RSA
CERES
MAGeCK RRA
CRISPhieRmix
MAGeCK MLE
CRISPRko
edgeR
MAGeCK
BAGEL

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