Welcome to the Multi-Dendrix documentation!

Contents:

• Installation instructions for Multi-Dendrix
  • Downloading and installing
  • System requirements
• Getting started
  • Running Multi-Dendrix
  • Improving runtime
• Multi-Dendrix Pipeline
  • Outline
  • Arguments
  • Script
• Input File Formats
  • Mutation data files
  • Protein-Protein Interaction (PPI) network files
• Output File Formats
  • Collections of gene sets
  • Subtype analysis
  • Permuted data
• Modules
  • Multi-Dendrix
  • (Sub)type-specific mutations
  • Permute mutation data
  • Matrix permutation test
  • Permute protein-protein interaction network
  • Direct interactions test
  • Core modules
  • Output functions
• Example uses of the Multi-Dendrix pipeline
  • Batch Multi-Dendrix
  • Analyzing subtype-specific mutations
  • Generating permutation data
  • Weight permutation test
  • Generating permuted networks
  • Direct interactions test
• Results from users
• Credits

Indices and tables

• Index
• Module Index
• Search Page