Welcome to cMonkey₂

This is the Python implementation of the cMonkey algorithm based on the original R implementation by David J. Reiss, Institute for Systems Biology.

cMonkey₂ supports Python 2.7.x and >= 3.3.

Contents:

• Installation
• Quick Start
• Walkthrough of a Complete cMonkey2 Run
  • Setting up for a cMonkey₂ run
  • Starting the run
  • Initialization steps
  • What is happening at each iteration
  • Inside a scoring module
  • Monitoring progress
  • Post-processing steps
  • Results data format
  • Viewing results
  • Plugging in cMonkey Results for downstream analysis
• cMonkey Principles
  • Core algorithm
  • Anatomy of a scoring module
  • System defined scoring modules
  • How to implement your own scoring module
• Configuration and Run Options
  • Command line options
  • Configuration (.ini) files
  • Useful configuration constructs
  • Scoring pipeline configuration (.json) files
  • Tricky topics
• Input File Formats
  • Gene expressions (mandatory)
  • RSAT information
  • STRING protein-protein interactions
• Result Database Schema
  • Introduction
  • Tables
• MEME Setup
  • MEME Suite notes
  • Installation script
  • MEME 4.3.0
  • MEME 4.8.x and later
• Set Enrichment Setup
  • How to setup set enrichment
• Visualize Results in cMonkey2 Viewer
  • Description
  • Views
• More Tips for Running, Debugging, Developing
  • Interactive exploration of results
  • Debugging
  • Data exchange

Indices and tables

• Index
• Module Index
• Search Page