CRISPR AnalyzeR for Pooled CRISPR Screens

CRISPR-Analyzer for pooled CRISPR screens (caRpools) provides an end-to-end analysis of CRISPR screens including quality control, hit candidate analysis, visualization and automated report generation using R markdown. Needs MAGeCK (, bowtie2 for all functions. CRISPR (clustered regularly interspaced short palindromic repeats) is a method to perform genome editing. See <> for more information on CRISPR.


Reference manual

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0.83 by Jan Winter, 6 years ago,

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Browse source code at

Authors: Jan Winter , Florian Heigwer

Documentation:   PDF Manual  

GPL license

Imports rmarkdown, VennDiagram, DESeq2, sm, biomaRt, seqinr, scatterplot3d, xlsx

Suggests BiocGenerics, knitr, stringi

System requirements: MAGeCK (=0.51, from, bowtie2 (

See at CRAN