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Welcome to the cmonkey-python Wiki!

1. Introduction

cMonkey is a machine learning algorithm and data integration framework which aims to discover co-regulated modules, or bicluster in gene expression profiles. It does so by integrating additional prior information such as operons, gene functions, or protein-protein interactions as well as the de novo detection of cis-regulatory DNA sequence motifs, and aggregate these into a combined score for improving the clustering.

Find here details about the usage of cmonkey-python

1. Selected Topics

• [Quickstart](wiki/quickstart)
• [Installation](wiki/installation)
• [Walkthrough of a Complete cMonkey Run](wiki/Walkthrough-of-a-Complete-cMonkey-Run)
• [cMonkey Principles](wiki/cMonkey-Principles)
• [Configuration and run options](wiki/configuration-and-run-options)
• [Standardized Input Data File Formats](wiki/input-file-formats)
• [Result Database Schema](wiki/database-schema)
• [Setting up a cMonkey/Python run](wiki/Setting-up-a-cMonkey-Python-run)
• [MEME Setup](wiki/MEME-Setup)
• [EC2 Setup](wiki/EC2-Setup)
• [Preparing STRING files](wiki/preparing-string-files)
• [Cluster Viewer](wiki/Cluster-Viewer)
• [More tips for running, debugging, developing](wiki/more-tips)
• [Source code documentation](http://networks.systemsbiology.net/static/cmonkey/cmonkey-pydoc/cmonkey.datamatrix.html)