We have been working on a new R package, genomation, that will help with the analysis of genomic intervals. Briefly, the package contains a collection of tools for visualizing and analyzing genome-wide data sets. The package works with a variety of genomic interval file types (BAM, bigWig, BED, GFF and any tabular format containing genomic locations) and enables easy summarization and annotation of high throughput data sets with given genomic annotations. Below is a presentation I'm preparing for an upcoming internal meeting. You can find more information and the vignette on the webpage.