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Welcome to the cmonkey-python Wiki!

Introduction

cMonkey is a machine learning based method to discover clusters for given gene expression profiles. It can also incorporate additional information such as operons or protein-protein interactions as well as biological motifs and aggregate these into a combined score for improving the clustering.

Find here details about the usage of cmonkey-python

Selected Topics

• cMonkey Principles
• Setting up a cMonkey/Python run
• MEME Setup
• EC2 Setup
• Preparing STRING files
• The JSON output file format
• Cluster Viewer
• More tips for running, debugging, developing