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City of Hope CpG Island Analysis Pipeline COHCAP

Provides tools for analysing single-nucleotide resolution methylation data. COHCAP is a pipeline that covers most user needs for differential methylation and integration with gene expression data. The software includes quality control metrics, defining differentially methylated CpG sites, defining differentially methylated CpG islands and visualization of methylation data. It contains two different methods of CpG island analysis. COHCAP has been shown scalable for high-quality integrative analysis of cell line data as well as large heterogeneous patient samples.

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COHCAP forum

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COHCAP classification

COHCAP specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
Java, Perl, R
Version:
1.20.0
Requirements:
WriteXLS, COHCAPanno, RColorBrewer, gplots
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

COHCAP distribution

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COHCAP support

Documentation

Maintainers

  • Charles Warden <>
  • Yate-Ching Yuan <>

Credits

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Publications

Institution(s)

Bioinformatics Core, City of Hope National Medical Center, Duarte, CA, USA; Department of Molecular Medicine, City of Hope National Medical Center, Duarte, CA, USA; Cancer Immunotherapeutics and Immunology, City of Hope National Medical Center, Duarte, CA, USA; Department of Biology, City of Hope National Medical Center, Duarte, CA, USA; Department of Diabetes and Metabolic Disease Research, City of Hope National Medical Center, Duarte, CA, USA; Functional Genomics Core, City of Hope National Medical Center, Duarte, CA, USA; Department of Molecular & Cellular Biology, City of Hope National Medical Center, Duarte, CA, USA

Funding source(s)

Supported by The National Institutes of Health [Comprehensive Cancer Center Grant P30 CA33572, R01 CA115674, R01 CA122976] and City of Hope National Medical Center [institutional funding].

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