DOI: 10.18129/B9.bioc.COHCAP  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see COHCAP.

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

Bioconductor version: 3.17

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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PDF R Script COHCAP Vignette
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biocViews DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Microarray, Software
Version 1.46.0
In Bioconductor since BioC 2.14 (R-3.1) (9.5 years)
License GPL-3
Depends WriteXLS, COHCAPanno, RColorBrewer, gplots
Imports Rcpp, RcppArmadillo, BH
LinkingTo Rcpp, BH
SystemRequirements Perl
Depends On Me
Imports Me
Suggests Me
Links To Me
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