Welcome to hicstuff’s documentation!

hicstuff is a python library to generate and manipulate Hi-C matrices. It aims to be easy to use and install. You can follow hicstuff’s development on Github .

Introduction

• Installation
• Quickstart
• hicstuff command line interface demo
  • Getting started
    • Using an indexed genome
    • Setting the binning
    • Temporary files
    • Additional options
  • Advanced usage
    • Starting from intermediate files
  • Generating the distance law
  • Operations on Hi-C matrices
    • Visualizing the matrix
    • Converting between formats
    • Rebinning existing matrices
    • Subsampling contacts
• hicstuff API demo
  • Data preparation
  • Full pipeline using the API
  • Visualise output files
    • Rebinning
    • Exporting
  • Playing with formats

Reference API

• hicstuff package
  • Submodules
  • hicstuff.commands module
  • hicstuff.digest module
  • hicstuff.distance_law module
  • hicstuff.filter module
  • hicstuff.hicstuff module
  • hicstuff.io module
  • hicstuff.iteralign module
  • hicstuff.main module
  • hicstuff.version module
  • hicstuff.view module
  • Module contents

Indices and tables

• Index
• Module Index
• Search Page