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CRISPRAnalyzeR: Interactive analysis, annotation and documentation of pooled CRISPR screens

Jan Winter, Marc Schwering, Oliver Pelz, Benedikt Rauscher, Tianzuo Zhan, Florian Heigwer, Michael Boutros
doi: https://doi.org/10.1101/109967
Jan Winter
1German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Germany
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Marc Schwering
1German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Germany
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Oliver Pelz
1German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Germany
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Benedikt Rauscher
1German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Germany
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Tianzuo Zhan
1German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Germany
2Department of Internal Medicine II, Medical Faculty Mannheim, Heidelberg University, Germany
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Florian Heigwer
1German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Germany
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Michael Boutros
1German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Germany
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Abstract

Pooled CRISPR/Cas9 screens are a powerful and versatile tool for the systematic investigation of cellular processes in a variety of organisms. Such screens generate large amounts of data that present a new challenge to analyze and interpret. Here, we developed a web application to analyze, document and explore pooled CRISR/Cas9 screens using a unified single workflow. The end-to-end analysis pipeline features eight different hit calling strategies based on state-of-the-art methods, including DESeq2, MAGeCK, edgeR, sgRSEA, Z-Ratio, Mann-Whitney test, ScreenBEAM and BAGEL. Results can be compared with interactive visualizations and data tables. CRISPRAnalyzeR integrates meta-information from 26 external data resources, providing a wide array of options for the annotation and documentation of screens. The application was developed with user experience in mind, requiring no previous knowledge in bioinformatics. All modern operating systems are supported.

Availability and online documentation: The source code, a pre-configured docker application, sample data and a documentation can be found on our GitHub page (http://www.github.com/boutroslab/CRISPRAnalyzeR). A tutorial video can be found at http://www.crispr-analyzer.org.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 20, 2017.
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CRISPRAnalyzeR: Interactive analysis, annotation and documentation of pooled CRISPR screens
Jan Winter, Marc Schwering, Oliver Pelz, Benedikt Rauscher, Tianzuo Zhan, Florian Heigwer, Michael Boutros
bioRxiv 109967; doi: https://doi.org/10.1101/109967
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CRISPRAnalyzeR: Interactive analysis, annotation and documentation of pooled CRISPR screens
Jan Winter, Marc Schwering, Oliver Pelz, Benedikt Rauscher, Tianzuo Zhan, Florian Heigwer, Michael Boutros
bioRxiv 109967; doi: https://doi.org/10.1101/109967

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