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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:

1) The standalone version of COHCAP is no longer being updated. Please see the Bioconductor version:

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

2) In addition to the original NAR paper, please see the following links:

Benchmarks: http://www.nature.com/protocolexchange/protocols/2965#/introduction

Protocol Exchange Files: http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip

EPIC Array Templates:

https://github.com/cwarden45/DNAmethylation_templates/tree/master/EPIC_workflow

https://github.com/cwarden45/DNAmethylation_templates/tre

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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