COHCAP (City of Hope CpG Island Analysis Pipeline, pronounced "co-cap") is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.).

Please note:

1) The SourceForge version of COHCAP is no longer being updated.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

https://github.com/cwarden45/COHCAP

This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through GitHub.

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

3) Custom Annotation Files (including EPIC Array):

https://sourceforge.net/projects/cohcap/files/additional_Bioconductor_annotations.zip/download

Features

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

Project Samples

COHCAP GUI with background window (PC) COHCAP GUI with background window (Mac) sample histogram dendrogram Box Plot Scatter Plot

Project Activity

See All Activity >

Categories

Bio-Informatics

License

Attribution Assurance License

Follow COHCAP

COHCAP Web Site

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Additional Project Details

Operating Systems

BSD, Windows

Languages

English

Intended Audience

Science/Research

User Interface

Java Swing

Programming Language

Java, Perl, S/R

Related Categories

Perl Bio-Informatics Software, Java Bio-Informatics Software, S/R Bio-Informatics Software

Registered

2012-10-23
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