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Installation

System Requirements

  • Python: 3.12 or 3.13 (3.14+ not yet supported due to PyO3 compatibility)
  • OS: Linux, macOS, or WSL on Windows
  • Disk: Sufficient space for BAM files and output Zarr datasets
  • RAM: 4 GB minimum (8+ GB recommended for large files)

Installation

conda create -n quantnado python=3.13
conda activate quantnado
conda install -c conda-forge quantnado

Or with mamba (faster):

mamba create -n quantnado -c conda-forge quantnado
mamba activate quantnado

Via Pip

pip install quantnado

From Source (Development)

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

# Install in editable mode with dev dependencies
pip install -e ".[dev]"

Verify Installation

quantnado --version
quantnado --help

Dependencies

Key dependencies installed automatically:

  • pysam - BAM file handling
  • pyBigWig - BigWig track handling
  • zarr - Data storage
  • dask - Parallel processing
  • xarray - Multidimensional arrays
  • pandas - Metadata handling

Troubleshooting Installation

Python 3.14 Compatibility Issue

If you see PyO3's maximum supported version (3.13) error, downgrade to Python 3.13:

conda install python=3.13

BAM Indexing Requirement

Your BAM files must be indexed (.bai files). If missing:

samtools index sample.bam

Missing Chromsizes File

Download chromsizes for your genome:

# Human hg38
curl -O ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes

# Or generate from FASTA
faidx --fetch-order genome.fasta | cut -f1,2 > genome.chrom.sizes
- xarray ≥ 2025.1.1 - Labeled arrays - dask ≥ 2024.1.0 - Lazy evaluation and parallel computing - pandas - Data structures - numpy - Numerical computing - pyranges ≥ 0.1.4 - Genomic ranges - scikit-learn - Machine learning (PCA)

Optional Dependencies

Development tools:

pip install quantnado[dev]

Verify Installation

Check that QuantNado is properly installed:

quantnado --version

quantnado --help

Next Steps

After installation, see: