Abstract
MOTIVATION: Next-generation sequencing methods continue improving the annotation of genomes in part by determining the distribution of features such as epigenetic marks. Evaluating and interpreting the association between genomic regions and their features has become a common and challenging analysis in genomic and epigenomic studies. RESULTS: With regioneR we provided an R package allowing to assess the statistical significance of pairwise associations between genomic region sets using permutation tests. We now present the R package regioneReloaded that builds upon regioneR's statistical foundation and extends the functionality for the simultaneous analysis and visualization of the associations between multiple genomic region sets. Thus, we provide a novel discovery tool for the identification of significant associations that warrant to be tested for functional interdependence. AVAILABILITY AND IMPLEMENTATION: regioneReloaded is an R package released under an Artistic-2.0 License. The source code and documentation are freely available through Bioconductor: http://www.bioconductor.org/packages/regioneReloaded.