MethylMix

MethylMix is an R package that identifies disease-specific hyper and hypomethylated genes. It uses a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix introduces a new metric, the Differential Methylation value (DM-value), defined as the difference of a methylation state with the normal methylation state. The tool utilizes matched gene expression data to identify differential and transcriptionally predictive methylation states by focusing on methylation changes that affect gene expression