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Installation

scpviz is distributed as a Python package and can be installed with pip.

pip install scpviz

This will install all required dependencies, including scanpy, anndata, pandas, and common plotting libraries.

Development installation

To install the latest development version directly from GitHub:

git clone https://github.com/gnaprs/scpviz.git
cd scpviz
pip install -e .

This installs scpviz in editable mode, so any changes to the code will be reflected immediately.

If you would like to contribute to scpviz, please see the Contributing Guide

Dependencies

  • Python ≥ 3.8
  • Core scientific stack: numpy, scipy, pandas
  • Data structures: anndata, scanpy
  • Plotting: matplotlib, seaborn, upsetplot
  • Network and enrichment: requests (for UniProt/STRING API access)

Optional dependencies

Some external functions (e.g. Leiden clustering or directLFQ normalization) may require internet access or additional packages. These are noted in the corresponding tutorial pages.