scspecies 0.1.0

scspecies allows users to align latent representations of single-cell datasets from different species.

scspecies

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.

Installation

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

# Without extras
pip install scspecies

# Installs visualization libraries
pip install scspecies[plotting]

# Notebook support. Installs Jupyter and related packages so you can run the example notebooks in the tutorials/ folder. Notebooks can be accessed via the package documentation or found in docs/source/tutorials via GitHub.
pip install scspecies[notebooks]

# All extras
pip install scspecies[plotting,notebooks]

After installing, confirm that scSpecies loads:

.. code-block:: bash

python -c "import scspecies; print(scspecies.__version__)"

Documentation

Full API docs, tutorials, and examples are available at: scSpecies Documentation (Read the Docs)