This is the Linux app named MethPipeline whose latest release can be downloaded as methpipeline.201708.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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Next-generation data pipeline to statistically call methylated and differentially methylated loci
See the manual in doc/manual.pdf
Calling of (differentially) methylated _positions_ will soon be uploaded.
This is an application that can also be fetched from https://sourceforge.net/projects/methpipeline/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.