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Genome Biol. 2015 Dec 16;16:281. doi: 10.1186/s13059-015-0843-6.

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

Li W1,2, Köster J1,2,3, Xu H4, Chen CH1,2, Xiao T2,3, Liu JS5, Brown M6,7,8, Liu XS9,10,11.

Author information

1
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
2
Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
3
Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
4
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.
5
Department of Statistics, Harvard University, Science Center 715, 1 Oxford Street, Cambridge, MA, 02138, USA.
6
Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. myles_brown@dfci.harvard.edu.
7
Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. myles_brown@dfci.harvard.edu.
8
Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02215, USA. myles_brown@dfci.harvard.edu.
9
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA. xsliu@jimmy.harvard.edu.
10
Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. xsliu@jimmy.harvard.edu.
11
School of Life Science and Technology, Tongji University, Shanghai, 200092, China. xsliu@jimmy.harvard.edu.

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 .

PMID:
26673418
PMCID:
PMC4699372
DOI:
10.1186/s13059-015-0843-6
[Indexed for MEDLINE]
Free PMC Article

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