COHCAP

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1) The SourceForge version of COHCAP is no longer being updated.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

Project Activity

See All Activity >

License

Attribution Assurance License

Follow COHCAP

COHCAP Web Site

Other Useful Business Software

MongoDB Atlas runs apps anywhere

Deploy in 115+ regions with the modern database for every enterprise.

MongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.

Start Free

Rate This Project

User Reviews

Be the first to post a review of COHCAP!

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

Similar Business Software

GenomeStudio

Visualize and analyze data generated on Illumina array platforms with GenomeStudio Software. This powerful solution supports the genotyping analysis of microarray data. Performance-optimized tools and a user-friendly graphical interface enable you to convert data into meaningful results quickly...

See Software
QIAGEN CLC Genomics Workbench

QIAGEN CLC Genomics Workbench is a powerful solution that works for everyone, no matter the workflow. Cutting-edge technology and unique features and algorithms widely used by scientific leaders in industry and academia make it easy to overcome challenges associated with data analysis....

See Software
Evo 2

Evo 2 is a genomic foundation model capable of generalist prediction and design tasks across DNA, RNA, and proteins. It utilizes a frontier deep learning architecture to model biological sequences at single-nucleotide resolution, achieving near-linear scaling of compute and memory relative to...

See Software
Illumina Connected Analytics

Store, archive, manage, and collaborate on multi-omic datasets. Illumina Connected Analytics is a secure genomic data platform to operationalize informatics and drive scientific insights. Easily import, build, and edit workflows with tools like CWL and Nextflow. Leverage DRAGEN bioinformatics...

See Software
Illumina DRAGEN Secondary Analysis

The Illumina DRAGEN Secondary Analysis provides accurate, comprehensive, and efficient analysis of next-generation sequencing data. Graph reference genome and machine learning driving unprecedented accuracy. Provides ultra-efficient workflow; can fully process a 34x whole human genome in ~30...

See Software
Evo Designer

Evo Designer is an advanced tool developed by the Arc Institute, leveraging the capabilities of the Evo 2 genomic foundation model to facilitate DNA sequence generation and analysis. This platform enables users to input nucleotide sequences or specify organisms, prompting the model to generate...

See Software