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.

Additional Metadata
Persistent URL dx.doi.org/10.1186/s13059-015-0843-6
Journal Genome Biology
Grant This work was funded by the The Netherlands Organisation for Scientific Research (NWO); grant id nwo/639.072.309 - Statistical Models for Structural Genetic Variants in the Genome of the Netherlands
Citation
Li, W. (Wei), Köster, J, Xu, H. (Han), Chen, C.-H. (Chen-Hao), Xiao, T. (Tengfei), Liu, J.S. (Jun), … Liu, X.S. (Shirley). (2015). Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR. Genome Biology, 16(1). doi:10.1186/s13059-015-0843-6