scSpecies is a deep‐learning framework for aligning single‐cell RNA-seq datasets across species.
Built on top of scVI and transfer-learning principles, it learns a shared embedding space that directly matches cell populations from different organisms.
To install the latest stable release of scSpecies run one of the following commands. scSpecies defines two extras required to run the tutorial notebooks, plotting and notebooks.
.. code-block:: bash
pip install scspecies
After installing, confirm that scSpecies loads:
.. code-block:: bash
python -c "import scspecies; print(scspecies.__version__)"
Full API docs, tutorials, and examples are available at: scSpecies Documentation (Read the Docs)
Start with running the tutorial notebooks. They can be downloaded from the GitHub repository.
The corresponding methodological paper is published in Genome Biology (2025): “scSpecies: enhancement of network architecture alignment in comparative single-cell studies”, DOI: 10.1186/s13059-025-03866-2.