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

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…

• NS
  National Science Foundation

  Award: DMS-1120368
• DC
  Dana-Farber Cancer Institute
• NI
  National Institutes of Health

  Awards: R01 GM113242-01, U01 CA180980
• NH
  National Human Genome Research Institute

  Award: R01 HG008728