PT  - JOURNAL ARTICLE
AU  - Jan Winter
AU  - Marc Schwering
AU  - Oliver Pelz
AU  - Benedikt Rauscher
AU  - Tianzuo Zhan
AU  - Florian Heigwer
AU  - Michael Boutros
TI  - CRISPRAnalyzeR: Interactive analysis, annotation and documentation of pooled CRISPR screens
AID  - 10.1101/109967
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 109967
4099  - http://biorxiv.org/content/early/2017/02/20/109967.short
4100  - http://biorxiv.org/content/early/2017/02/20/109967.full
AB  - 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.