MOTIVATION: Statistically assessing the relation between a set of genomic 
regions and other genomic features is a common challenging task in genomic and 
epigenomic analyses. Randomization based approaches implicitly take into account 
the complexity of the genome without the need of assuming an underlying 
statistical model.
SUMMARY: regioneR is an R package that implements a permutation test framework 
specifically designed to work with genomic regions. In addition to the 
predefined randomization and evaluation strategies, regioneR is fully 
customizable allowing the use of custom strategies to adapt it to specific 
questions. Finally, it also implements a novel function to evaluate the local 
specificity of the detected association.
AVAILABILITY AND IMPLEMENTATION: regioneR is an R package released under 
Artistic-2.0 License. The source code and documents are freely available through 
Bioconductor (http://www.bioconductor.org/packages/regioneR).
CONTACT: rmalinverni@carrerasresearch.org.