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Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout MAGeCK

Identifies positively and negatively selected sgRNAs and genes in genome-scale CRISPR/Cas9 knockout experiments. MAGeCK consists of four steps: read count normalization, mean-variance modeling, sgRNA ranking and gene ranking. The software results are robust across different sequencing depths and numbers of sgRNAs per gene. It is also able to perform both positive and negative selection screens simultaneously, and identify biologically meaningful and cell type-specific essential genes and pathways.

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MAGeCK forum

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MAGeCK versioning

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MAGeCK classification

MAGeCK specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C, Python
Computer skills:
Advanced
Stability:
Stable
Source code URL:
https://sourceforge.net/projects/mageck/files/0.5/mageck-0.5.6.tar.gz/download
Conda:
https://bioconda.github.io/recipes/mageck/README.html
Interface:
Command line interface
Operating system:
Unix/Linux
License:
BSD 2-clause “Simplified” License
Version:
0.5.6
Maintained:
Yes

MAGeCK support

Documentation

Maintainer

  • Wei Li <>

Credits

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Publications

Institution(s)

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA

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