Requirements

The list of package version requirements is available in setup.py, and will be automatically installed along PyDESeq2 when using PyPI. For reference, the code was tested with python 3.11 and the following package versions:

- anndata>=0.11.0
- formulaic>=1.0.2
- numpy>=2.0.0
- pandas>=2.2.0
- scikit-learn>=1.4.0
- scipy>=1.12.0
- formulaic-contrasts>=0.2.0
- matplotlib>=3.9.0

Note that starting from pydeseq2 0.5.3, python 3.10 is no longer supported. Please don’t hesitate to open an issue in case you encounter any problems due to possible deprecations.