Gunz-CM: Matrix Math for Genomics

Gunz-CM is a high-performance Python library for loading, manipulating, and filtering genomic contact matrices. It provides unified support for all major formats, including .hic, .cool, and .csv.

The Gunz Ecosystem

• Gunz-ML (SDK)
• Gunz-CM (Matrix)
• Gunz-Utils (Core)

Getting Started

• Getting Started with Gunz-CM
• Installation
• Quickstart
• Core Concepts

User Guide

• User Guide
  • Pipeline overview
  • Module index
  • How to use this guide
  • Where to go next

Technical Reference

• GZCM Format
  • Version Overview
  • File Layout
  • Header Schema
  • Version Details
  • CLI Usage
  • Python API
  • Supported Codecs (v3)
  • Compression Ratios
  • See Also
• gunz_cm
  • gunz_cm package
• Tutorials
  • The pipeline
  • What you need
  • Why the tutorials are pre-rendered
  • Pre-existing bugs documented in the tutorials
  • Where to go next

Tutorials

• Tutorials
• Tutorial: Load HIC contact matrix data
• Tutorial: Convert contact matrices to alternate formats
• Tutorial: Visualizing Hi-C contact matrices with gunz_cm.visualizations
• Tutorial: Filter and balance a contact matrix
• Tutorial: KR and ICE balancing for Hi-C contact matrices
• Tutorial: Downsample a Hi-C contact matrix to a coarser resolution

Project Info

• Changelog

Indices and tables

• Index

• Module Index

• Search Page