Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It also includes data from the Gene Expression Barcode project for transcriptome visualization. It has a flexible plugin framework so users can add d3 visualizations. You can find more information about Epiviz at http://epiviz.github.io and see a video tour here.

The Epivizr Bioconductor package implements two-way
communication between the R/Bioconductor computational genomics environment and EpiViz. Objects in an R session
can be displayed as tracks or plots on EpiViz. Epivizr uses WebSockets for communication
between the browser JavaScript client and the R environment.