Methods Mol Biol

Arrays provide a cost-effective platform for the analysis of human DNA methylation. ShinyEPICo is an interactive, web-based, and graphical tool that allows the user to analyze Illumina DNA methylation arrays (450k and EPIC), from the user's own computer or from a server. This tool covers the analysis entirely, from the raw data input to the final list of differentially methylated positions or regions. Here, we describe the steps of the analysis, the different parameters available, and useful information to understand and select the best options in each step.