COHCAP (City of Hope CpG Island Analysis Pipeline, pronounced "co-cap") is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.).
Please note:
1) The SourceForge version of COHCAP is no longer being updated. 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
Features
- DNA methylation analysis
- integration of methylation and gene expression data
- graphical user interface for basic users