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...Please see the GitHub version:
https://github.com/cwarden45/COHCAP
This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through GitHub.
2) 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