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.
genomation is published in Bioinformatics
Akalin A, Franke V, Vlahoviček K, Mason CE, Schübeler D. genomation: a toolkit to summarize, annotate and visualize genomic intervals. Bioinformatics. 2014 Nov 21. pii: btu775
It is also currently in the Bioconductor development version