Installation

Gunz-CM is a high-performance library for genomic contact matrix manipulation. It requires Python 3.11 or higher.

Standard Installation

Install the library directly from GitHub:

pip install git+https://github.com/sXperfect/gunz-cm.git

Recommended: Mamba/Conda Environment

We recommend using a dedicated mamba environment to ensure high-performance linear algebra libraries (like OpenBLAS or MKL) are correctly linked:

# Create the environment
mamba create -n gunz-cm python=3.11

# Activate it
mamba activate gunz-cm

# Install in editable mode for research
pip install -e .

Optional Dependencies

Genomics data processing often requires specialized file formats and visualization tools. Install them using the following tags:

[conv]: Support for .hic to .cool conversion.
[vis]: Matplotlib, Plotly, and Interactive widgets.
[all]: Recommended for full research capability.

pip install "gunz-cm[all]"

System Dependencies

Some components (like pybedtools) require C++ compilers and compression libraries:

Ubuntu/Debian: sudo apt-get install g++ libcurl4-openssl-dev