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

By Wei Li, Johannes Köster, Han Xu, Chenhao Chen, Tengfei Xiao, Jun S. Liu, Myles A. Brown, X. S. Liu. Genome Biology, 2015

422 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/c397e23af316388e20ebcbad04fab1516d2ec783

Citations in the corpus

• When Risks Cannot Be Seen: Regulating Uncertainty in Emerging Technologies (2017, neutral): “Conversely, in other manufacturing processes like MAM or genetic engineering (Li et al., 2015), testing can be challenging or impossible mid-process, and is mainly performed at the end of the process.”