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

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

Authors

Wei Li^{1

2}, Johannes Köster^{1

2

3}, Han Xu⁴, Chen-Hao Chen^{1

2}, Tengfei Xiao^{2

3}, Jun S Liu⁵, Myles Brown^{6

7

8}, X Shirley Liu^{9

10

11}

Affiliations

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. [email protected].
⁷ Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. [email protected].
⁸ Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02215, USA. [email protected].
⁹ Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA. [email protected].
¹⁰ Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. [email protected].
¹¹ School of Life Science and Technology, Tongji University, Shanghai, 200092, China. [email protected].

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 .

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

CRISPR-Cas Systems*
Gene Targeting / methods*
Gene Targeting / standards
Genes, Essential
Quality Control
Software*

Abstract

Publication types

MeSH terms

Grants and funding