dmml - A maximum-likelihood method for identifying differential methylation in samples with varying tumor purity
dmml is a tool for identifying differentially methylated sites in tumor samples with varying, unknown tumor cell fraction using a maximum-likelihood method. For the details about the method and validation, please refer to our publication on the matter.
Major features:
Comparison of up to 31 tumor samples simultaneously
Zero, one, or multiple control samples
Tumor purity of each sample is automatically estimated; alternatively, prior knowledge about the tumor cell fraction can be injected
The estimator models co-methylation of neighboring sites locally in each neighborhood, which properly accounts for correlations within and across CG islands