Title |
Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR
|
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Published in |
Genome Biology, December 2015
|
DOI | 10.1186/s13059-015-0843-6 |
Pubmed ID | |
Authors |
Wei Li, Johannes Köster, Han Xu, Chen-Hao Chen, Tengfei Xiao, Jun S. Liu, Myles Brown, X. Shirley Liu |
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 . |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 2 | 20% |
India | 1 | 10% |
United Kingdom | 1 | 10% |
Unknown | 6 | 60% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 6 | 60% |
Scientists | 3 | 30% |
Science communicators (journalists, bloggers, editors) | 1 | 10% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
China | 2 | <1% |
Switzerland | 1 | <1% |
Germany | 1 | <1% |
Canada | 1 | <1% |
United States | 1 | <1% |
Unknown | 487 | 99% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 130 | 26% |
Researcher | 108 | 22% |
Student > Master | 52 | 11% |
Student > Bachelor | 36 | 7% |
Student > Doctoral Student | 23 | 5% |
Other | 48 | 10% |
Unknown | 96 | 19% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 185 | 38% |
Agricultural and Biological Sciences | 101 | 20% |
Medicine and Dentistry | 25 | 5% |
Immunology and Microbiology | 16 | 3% |
Computer Science | 15 | 3% |
Other | 51 | 10% |
Unknown | 100 | 20% |