caRpools: an R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens

Jan Winter; Marco Breinig; Florian Heigwer; Dirk Brügemann; Svenja Leible; Oliver Pelz; Tianzuo Zhan; Michael Boutros

doi:10.1093/bioinformatics/btv617

caRpools: an R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens

Bioinformatics. 2016 Feb 15;32(4):632-4. doi: 10.1093/bioinformatics/btv617. Epub 2015 Oct 27.

Authors

Jan Winter¹, Marco Breinig¹, Florian Heigwer¹, Dirk Brügemann¹, Svenja Leible¹, Oliver Pelz¹, Tianzuo Zhan², Michael Boutros¹

Affiliations

¹ German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Heidelberg, Germany and.
² German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Heidelberg, Germany and Department of Medicine II, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.

PMID: 26508755
DOI: 10.1093/bioinformatics/btv617

Abstract

Motivation: Genetic screens by CRISPR/Cas9-mediated genome engineering have become a powerful tool for functional genomics. However, there is currently a lack of end-to-end software pipelines to analyze CRISPR/Cas9 screens based on next generation sequencing.

Results: The CRISPR-AnalyzeR for pooled screens (caRpools) is an R package for exploratory data analysis that provides a complete workflow to analyze CRISPR/Cas9 screens. To further support the analysis of large-scale screens, caRpools integrates screening documentation and generation of standardized analysis reports.

Availability and implementation: caRpools, manuals and an open virtual appliance are available at http://github.com/boutroslab/caRpools.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

CRISPR-Cas Systems*
Documentation
Gene Editing*
Genome
High-Throughput Nucleotide Sequencing
Software*