title: Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR.
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 .
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.|Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.|Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.|Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
authors.forename: Johannes
authors.initials: J
authors.lastname: Köster
authors.affiliation: Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.
authors.forename: Han
authors.initials: H
authors.lastname: Xu
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.|Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
authors.forename: Chen-Hao
authors.initials: CH
authors.lastname: Chen
authors.affiliation: Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.|Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
authors.forename: Tengfei
authors.initials: T
authors.lastname: Xiao
authors.affiliation: Department of Statistics, Harvard University, Science Center 715, 1 Oxford Street, Cambridge, MA, 02138, USA.
authors.forename: Jun S
authors.initials: JS
authors.lastname: Liu
authors.affiliation: Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. myles_brown@dfci.harvard.edu.|Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. myles_brown@dfci.harvard.edu.|Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02215, USA. myles_brown@dfci.harvard.edu.
authors.forename: Myles
authors.initials: M
authors.lastname: Brown
authors.affiliation: 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.|Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. xsliu@jimmy.harvard.edu.|School of Life Science and Technology, Tongji University, Shanghai, 200092, China. xsliu@jimmy.harvard.edu.
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D064113:CRISPR-Cas Systems; D018390:Gene Targeting / Q000379:methods* / Q000592:standards; D020043:Genes, Essential; D011786:Quality Control; D012984:Software