R package for comprehensive analysis of DNA methylation data obtained by Infinium microarrays and bisulfite sequencing protocols. RnBeads implements a series of QC steps and comprehensively outputs a number of analyses levels as annotated and readable hypertext report. RnBeads is the standard preparation tool for DNA-methylation data obtained by DEEP (German Epigenome Programme).
Assenov, Y., Müller, F., Lutsik, P., Walter, J., Lengauer, T., & Bock, C. (2014). Comprehensive analysis of DNA methylation data with RnBeads. Nature Methods, 11(11), 1138–1140.