Welcome to chess-hic’s documentation!

• Getting started with chess-hic
  • Overview
  • Installation
    • Prerequisites
    • Installation from the Python Package Index (PyPi)
    • Installation from source
  • Example analysis
    • Finding differences between samples of different conditions
• The chess-hic command line tool
  • chess pairs
    • Positional Arguments
    • Named Arguments
  • chess sim
    • Positional Arguments
    • Named Arguments
  • chess extract
    • Positional Arguments
    • Named Arguments
  • chess crosscorrelate
    • Positional Arguments
• FAQ
  • Why is chess sim so slow?
  • Why do I get “ERROR No valid region pairs found” when using Juicer .hic files?
  • Can I use CHESS to compare the results of loop calling software between samples?
  • I used the SSIM Z-score and SN thresholds from the CHESS paper. Why don’t I see any differences?
  • How do I choose an appropriate SSIM / SN threshold for my data?
  • What if I don’t have biological replicates?

Indices and tables

• Index
• Module Index
• Search Page