CHARMtools Documentation

Single-cell Hi-C and Multi-omics Data Analysis and Visualization Toolkit

Welcome to the CHARMtools documentation! CHARMtools is a comprehensive toolkit designed for single-cell Hi-C and multi-omics data analysis, providing end-to-end solutions from data preprocessing to advanced analysis and visualization.

📚 Documentation Structure

This documentation is organized into several sections to help you get started and make the most of CHARMtools:

Getting Started

• Installation Guide - Complete installation instructions and requirements
• Quick Start - Get up and running with CHARMtools in minutes
• Tutorial - Step-by-step tutorials for common workflows

Core Modules

• Cell3D Objects - Working with 3D chromatin structure data
• Data Preprocessing - Clean and prepare your Hi-C data
• Analysis Tools - Statistical analysis and computational methods
• Utilities - Helper functions and I/O operations

Advanced Topics

• API Reference - Complete API documentation
• Command Line Interface - Using CHARMtools from the command line
• Examples - Real-world usage examples and case studies

Development

• Contributing - How to contribute to CHARMtools
• Development Guide - Setting up development environment

✨ Key Features

🧬 3D Chromatin Structure Analysis

• Load and manipulate 3D genome structures
• Spatial analysis and clustering
• Structure visualization and export
• Multi-cell comparison and analysis

🔧 Data Preprocessing

• Clean promiscuous legs and artifacts
• Remove exon splicing contamination
• Filter isolated contact points
• Convert between data formats (3DG, pairs, etc.)

📊 Statistical Analysis

• Regression analysis and modeling
• TSS enrichment analysis
• Spatial statistical methods
• Differential analysis between conditions
• Single-cell specific analyses (scGAD, scAB)

🎨 Visualization

• Interactive 3D structure plots
• Contact matrix heatmaps
• Statistical plots and charts
• Customizable color schemes

🖥️ User-Friendly Interface

• Python API for programmatic access
• Command-line tools for batch processing
• Jupyter notebook integration
• Comprehensive documentation and examples

🚀 Quick Navigation

I want to...	Go to...
Install CHARMtools	Installation Guide
Learn the basics	Quick Start
Work with 3D structures	Cell3D Objects
Preprocess Hi-C data	Data Preprocessing
Perform statistical analysis	Analysis Tools
Use command-line tools	Command Line Interface
Find specific functions	API Reference
See real examples	Examples
Contribute to the project	Contributing

📋 System Requirements

• Python: 3.7 or higher
• Operating System: Linux, macOS, Windows
• Memory: 8GB RAM minimum (16GB+ recommended for large datasets)
• Storage: 1GB for installation, additional space for data
• Optional: R environment for some analysis modules

🆘 Getting Help

If you need help or have questions:

1. Check the documentation - Most common questions are answered here
2. Browse examples - See Examples for real-world usage
3. Search issues - Check GitHub Issues
4. Ask questions - Open a new issue or discussion
5. Contact us - Email: [email protected]

📄 License

CHARMtools is released under the MIT License. See the LICENSE file for details.

🙏 Acknowledgments

CHARMtools is developed and maintained by the CHARMtools development team. We thank all contributors and users for their support and feedback.

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Ready to get started? Head over to the Installation Guide to begin your journey with CHARMtools!