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This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see .

CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data

Bioconductor version: Development (3.19)

COHCAP (pronounced "co-cap") provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k/EPIC methylation array, targeted BS-Seq, etc.). It provides differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, with visualizaton options. Discussion Group:

Author: Charles Warden <cwarden at>, Yate-Ching Yuan <yyuan at>, Xiwei Wu <xwu at>

Maintainer: Charles Warden <cwarden at>

Citation (from within R, enter citation("COHCAP")):


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COHCAP Vignette PDF R Script
Reference Manual PDF


biocViews DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Microarray, Software
Version 1.49.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License GPL-3
Depends WriteXLS, COHCAPanno, RColorBrewer, gplots
Imports Rcpp, RcppArmadillo, BH
System Requirements Perl
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