Full analysis of whole-genome DNA methylation data
RnBeads is an R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution, including Infinium 450K microarray and bisulfite sequencing protocols, but also MeDIP-seq and MBD-seq once the data have been preprocessed with DNA methylation inference software. RnBeads implements an analysis workflow that is significantly more comprehensive than those of existing tools. It documents its results in a highly annotated and readable hypertext report, and it scales to the large sample sizes that are becoming the norm for DNA methylation analysis in human cohorts.
Note, RnBeads package as well as the current wrapper are still in testing phase, so the optimal performance may not be reached at the moment.