SUMMARY: Copy number variation (CNV) is a major type of structural genomic 
variation that is increasingly studied across different species for association 
with diseases and production traits. Established protocols for experimental 
detection and computational inference of CNVs from SNP array and next-generation 
sequencing data are available. We present the CNVRanger R/Bioconductor package 
which implements a comprehensive toolbox for structured downstream analysis of 
CNVs. This includes functionality for summarizing individual CNV calls across a 
population, assessing overlap with functional genomic regions, and genome-wide 
association analysis with gene expression and quantitative phenotypes.
AVAILABILITY AND IMPLEMENTATION: http://bioconductor.org/packages/CNVRanger.