Welcome to the optimalTAD documentation!

optimalTAD is an algorithm developed for finding the optimal set of topologically associated domains (TADs) based on a combination of Hi-C and epigenetic data.

Contents:

• Requirements
  • MPICH installation
  • Boost installation
• Installation
• Input Format
  • Hi-C data
  • ChIP-seq data
• Configuration file
• Usage
  • Optimization mode
  • Visualization mode
• Example usage
  • Optimization mode
  • Visualization mode

How to cite?