COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.
1) The standalone version of COHCAP is no longer being updated. Please see the Bioconductor version:
2) In addition to the original NAR paper, please see the following links:
Protocol Exchange Files: http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip
EPIC Array Templates:
- DNA methylation analysis
- integration of methylation and gene expression data
- graphical user interface for basic users
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