HiCAGE: an R package for large-scale annotation and visualization of 3C-based genomic data

Chromatin interactions measured by the 3C-based family of next generation technologies are becoming increasingly important for measuring the physical basis for regulatory interactions between different classes of functional domains in the genome. Software is needed to streamline analyses of these data and integrate them with custom genome annotations, RNA-seq, and gene ontologies. We introduce a new R package compatible with Bioconductor--Hi-C Annotation and Graphics Ensemble (HiCAGE)--to perform these tasks with minimum effort. In addition, the package contains a shiny/R web app interface to provide ready access to its functions.\n\nAvailability and ImplementationThe software is implemented in R and is freely available under GPLv3. HiCAGE runs in R (version 3.4) and is freely available through github (https://github.com/mworkman13/HiCAGE) or on the web (https://junkdnalab.shinyapps.io/hicage).