Li, WeiKöster, JohannesXu, HanChen, Chen-HaoXiao, TengfeiLiu, JunBrown, MylesLiu, X. Shirley2016-02-012015Li, 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/s13059-015-0843-6.1474-7596http://nrs.harvard.edu/urn-3:HUL.InstRepos:24984008High-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.en-USCRISPR/Cas9ScreeningMaximum likelihoodExpectation-MaximizationNegative binomialData-driven documentsD3VisualizationQuality controlJournal Article2016-02-0110.1186/s13059-015-0843-6