EPIPE is a bioinformatics pipeline designed for the analysis of methylation data obtained from microarrays. It implements the whole methylation array workflow steps from processing raw data to pathway annotation of the differentially methylation positions (DMP) and regions (DMR) found.
The main reasons to use it are:
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It supports multiple array platforms including 450K, EPIC and EPICv2.
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It automatically generates reports: Two reports are generated containing all the essential results of the analysis, facilitating an easy interpretation and presentation of findings. These reports are designed to meet the specific needs of collaborators and analysts, providing different levels of detail.
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It is customizable: Through the configuration settings script (config.R), users have the option to specify some preference parameters for the analysis.