RT Journal
A1 Allen, Felicity
A1 Khodak, Anton
A1 Behan, Fiona
A1 Iorio, Francesco
A1 Yusa, Kosuke
A1 Garnett, Mathew
A1 Parts, Leopold
T1 JACKS: joint analysis of CRISPR/Cas9 knockout screens
JF Genome Research 
JO Genome Research 
YR 2019 
FD January 23 
DO 10.1101/gr.238923.118 
SP gr.238923.118 
UL http://genome.cshlp.org/content/early/2019/01/23/gr.238923.118.abstract 
AB CRISPR/Cas9 knockout screens are revolutionizing mammalian functional genomics. Their range of applications remains limited by signal variability from different guideRNAs that target the same gene, which confounds gene effect estimation, and dictates large experiment sizes. To address this problem, we report JACKS, a Bayesian method that jointly analyzes screens performed with the same guide RNA library.  Modeling the variable guide efficacies greatly improves hit identification over processing a single screen at a time, and outperforms existing methods. This more efficient analysis gives additional hits, and allows designing libraries with a 2.5-fold reduction in required cell numbers without sacrificing performance compared to current analysis standards.