scArches 0.1.1

Transfer learning with Architecture Surgery on Single-cell data

|PyPI| |travis| |Docs|

scArches - single-cell architecture surgery

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scArches is a package to integrate newly produced single-cell datasets into integrated references atlases. Our method can facilitate large collaborative projects with decentralise training and integration of multiple datasets by different groups. scArches is compatible with scanpy <https://scanpy.readthedocs.io/en/stable/>_. and hosts efficient implementations of all conditional generative models for single-cell data.

What can you do with scArches?

• Integrate many single-cell datasets and share the trained model and the data (if possible).
• Download a pre-trained model for your atlas of interest, update it wih new datasets and share with your collaborators.
• Project and integrate query datasets on the top of a reference and use latent repesentation for downstream tasks, e.g.: diff testing, clustering.

Usage

See here <https://scarches.readthedocs.io/>_ for documentation and tutorials.

Support and contribute

If you have a question or new architchuture or a model that could be integrated in to our pipe-line, you can post an issue <https://github.com/theislab/scarches/issues/new>__ or reach us by email <mailto:[e-mail]>_. Our package support tf/keras now but pytorch version will be added very soon.

Reference

.. |PyPI| image:: https://img.shields.io/pypi/v/scarches.svg :target: https://pypi.org/project/scarches

.. |PyPIDownloads| image:: https://pepy.tech/badge/scarches :target: https://pepy.tech/project/scarches

.. |Docs| image:: https://readthedocs.org/projects/scarches/badge/?version=latest :target: https://scarches.readthedocs.io

.. |travis| image:: https://travis-ci.com/theislab/scarches.svg?branch=master :target: https://travis-ci.com/theislab/scarches