COHCAP

City of Hope CpG Island Analysis Pipeline

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Description

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.

Please note: It is now recommended that you use the Bioconductor version of COHCAP:

http://bioconductor.org/packages/release/bioc/html/COHCAP.html

If you use COHCAP please cite:

Charles D. Warden, Heehyoung Lee, Joshua D. Tompkins, Xiaojin Li, Charles Wang, Arthur D. Riggs, Hua Yu, Richard Jove, Yate-Ching Yuan. (2013) COHCAP: An Integrative Genomic Pipeline for Single-Nucleotide Resolution DNA Methylation Analysis. Nucleic Acids Research. 41 (11): e117

COHCAP Web Site

Features

  • DNA methylation analysis
  • integration of methylation and gene expression data
  • graphical user interface for basic users

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Additional Project Details

Languages

English

Intended Audience

Science/Research

User Interface

Java Swing

Programming Language

Perl, Java, S/R

Registered

2012-10-23
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