Installation

Requirements

• Python 3.12 or 3.13
• Linux, macOS, or WSL
• Indexed BAM files for BAM-based assays

Install from PyPI

pip install quantnado

Optional Extras

# Peak calling with LanceOTron
pip install "quantnado[lanceotron]"

# Documentation and development tooling
pip install -e ".[dev]"

# Example notebook tooling
pip install "quantnado[example]"

Install from Source

git clone https://github.com/Milne-Group/QuantNado.git
cd QuantNado
pip install -e .

Verify the Install

quantnado --version
quantnado --help

Notes

• BAM inputs must be coordinate-sorted and indexed with .bai.
• If you omit --chromsizes, QuantNado infers chromosome sizes from BAM headers or VCF contig headers when possible.
• quantnado[lanceotron] adds PyTorch-based peak calling support.

Next Steps

• Quick Start
• Usage Guide
• CLI Overview