methylKit: R package for DNA methylation analysis

High-throughput bisulfite sequencing based methods are popular for measuring genome-wide DNA methylation levels. Here is an R package that helps with the analysis of such DNA methylation data. Although, it is still under heavy development current functionality allows users to do many of the essential data analysis tasks. The package is primarily designed for Reduced Representation Bisulfite Sequencing (RRBS), however it can also handle whole-genome bisulfite sequencing if proper input format is provided.

Functionality includes:

• Read coverage statistics
• Methylation statistics
• Sample correlation and clustering
• Differential methylation analysis
• Feature annotation and accessor/coercion functions 
• Multiple visualization options 
• Regional and tiling windows analysis
• (Almost) proper documentation 

The package is here:
http://code.google.com/p/methylkit/