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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.