COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution methylation data. It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.
You can use COHCAP to analyze the following data types:
- Illumina Methylation Array (450k, 27k, etc.)
- Targeted BS-Seq
Integration with gene expression is suitable for any platform (Microarray, RNA-Seq, etc.).
There are two ways that you can use COHCAP
1) Standalone Version
Download here: https://sourceforge.net/projects/cohcap/
- Can be run via command line or GUI for basic users without coding experience (see below)
- Detailed documentation available through the following links
-FAQ Page: https://sourceforge.net/p/cohcap/wiki/Home/ -Discussion Group: https://sourceforge.net/p/cohcap/discussion/
2) Bioconductor Package
Download here: http://bioconductor.org/packages/devel/bioc/html/COHCAP.html
- Easy to Install
- Convenient for R users
- Protocol Exchange listing providing step-by-step instructions on anlayze on how to analyze Illumina 450k Methylation Array data using the Bioconductor package: http://dx.doi.org/10.1038/protex.2014.002
-The introduction also includes some simple benchmarks against other programs (IMA, ChAMP, minfi/bumphunter, RnBeads) as well as a link to template scripts to run the benchmarks yourself
Reference: Warden CD, Lee H, Tompkins JD, Li X, Wang C, Riggs AD, Yu H, Jove R, Yuan YC. (2013) COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis. Nucleic Acids Res. 41(11):e11
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