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Li, W. (Wei), J. Köster (Johannes), Xu, H. (Han), Chen, C.-H. (Chen-Hao), Xiao, T. (Tengfei), Liu, J.S. (Jun), Brown, M. (Myles) and Liu, X.S. (Shirley)

2015-12-16

Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR

Publication

Publication

Genome Biology , Volume 16 - Issue 1 p. 281:1- 281:13

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 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), 281:1–281:13. doi:10.1186/s13059-015-0843-6


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