COHCAP
City of Hope CpG Island Analysis Pipeline
...) In addition to the original NAR paper, please see the following links:
Benchmarks: http://www.nature.com/protocolexchange/protocols/2965#/introduction
Protocol Exchange Files: http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip
3) Custom Annotation Files (including EPIC Array):
https://sourceforge.net/projects/cohcap/files/additional_Bioconductor_annotations.zip/download