Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Li, Wei; Köster, Johannes; Xu, Han; Chen, Chen-Hao; Xiao, Tengfei; Liu, Jun; Brown, Myles; Liu, X.
• Is Part Of: Genome biology. Volume 16:Issue 1(2015)
• Page Start: 1
• Page End: 13
• Publication Date: 2015-12
• Subjects: CRISPR/Cas9 -- Screening -- Maximum likelihood -- Expectation-Maximization -- Negative binomial -- Data-driven documents -- D3 -- Visualization -- Quality control; Genomes -- Periodicals; Biology -- Periodicals; Molecular biology -- Periodicals; 572.8633
• DOI: 10.1186/s13059-015-0843-6
• Languages: English
• ISSNs: 1474-760X

Abstract

Abstract High-throughput CRISPR screens have shown great promise in functional genomics. We present MAGeCK-VISPR, a comprehensive quality control (QC), analysis, and visualization workflow for CRISPR screens. MAGeCK-VISPR defines a set of QC measures to assess the quality of an experiment, and includes a maximum-likelihood algorithm to call essential genes simultaneously under multiple conditions. The algorithm uses a generalized linear model to deconvolute different effects, and employs expectation-maximization to iteratively estimate sgRNA knockout efficiency and gene essentiality. MAGeCK-VISPR also includes VISPR, a framework for the interactive visualization and exploration of QC and analysis results. MAGeCK-VISPR is freely available athttp://bitbucket.org/liulab/mageck-vispr .