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

Wei Li; Johannes Köster; Han Xu; Chen Hao Chen; Tengfei Xiao; Jun S. Liu; Myles Brown; X. Shirley Liu

doi:10.1186/s13059-015-0843-6

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

Wei Li, Johannes Köster, Han Xu, Chen Hao Chen, Tengfei Xiao, Jun S. Liu, Myles Brown, X. Shirley Liu

Research output: Contribution to journal › Article › peer-review

240 Scopus citations

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.

Original language	English (US)
Article number	281
Journal	Genome biology
Volume	16
Issue number	1
DOIs	https://doi.org/10.1186/s13059-015-0843-6
State	Published - Dec 16 2015
Externally published	Yes

Keywords

CRISPR/Cas9
D3
Data-driven documents
Expectation-Maximization
Maximum likelihood
Negative binomial
Quality contro
Screening
Visualization

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/s13059-015-0843-6

Cite this

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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.",

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AU - Xu, Han

AU - Chen, Chen Hao

AU - Xiao, Tengfei

AU - Liu, Jun S.

AU - Brown, Myles

AU - Liu, X. Shirley

PY - 2015/12/16

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

Abstract

Keywords

ASJC Scopus subject areas

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