Chr3D is a Python framework for 3D chromatin interaction analysis. Process Hi-C, ChIA-PET, and HiChIP data with a unified command-line interface and Python API.

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Features

Command Line Interface

Run complete pipelines with a single command:

• chr3d bulk-hic - Bulk Hi-C processing
• chr3d sn-hic - Single-nucleus Hi-C
• chr3d chia-pet - ChIA-PET analysis
• chr3d hichip - HiChIP pipeline

View CLI Documentation →

Python API

Build custom workflows with modular components:

• Pipeline orchestrators
• Alignment and processing tools
• Matrix generation and analysis
• Peak calling and loop detection

View API Documentation →

Visualization

Export results for HiGlass and other genome browsers.

Quick Start

# Install
pip install chr3d
 
# Run a pipeline
chr3d bulk-hic \
    --r1 sample_R1.fastq.gz \
    --r2 sample_R2.fastq.gz \
    --genome hg38.fa \
    --output-dir ./results

Installation Guide →