Publication: Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR
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Date
2015
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BioMed Central
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Citation
Li, Wei, Johannes Köster, Han Xu, Chen-Hao Chen, Tengfei Xiao, Jun S. Liu, Myles Brown, and X. Shirley Liu. 2015. “Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR.” Genome Biology 16 (1): 281. doi:10.1186/s13059-015-0843-6. http://dx.doi.org/10.1186/s13059-015-0843-6.
Research Data
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 at http://bitbucket.org/liulab/mageck-vispr. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0843-6) contains supplementary material, which is available to authorized users.
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Keywords
CRISPR/Cas9, Screening, Maximum likelihood, Expectation-Maximization, Negative binomial, Data-driven documents, D3, Visualization, Quality control
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