Metadata-Version: 2.1
Name: scArches
Version: 0.6.1
Summary: Transfer learning with Architecture Surgery on Single-cell data
Home-page: https://github.com/theislab/scarches
Author: 
Author-email: 
License: MIT
Classifier: Programming Language :: Python :: 3.9
Classifier: Environment :: Console
Classifier: Framework :: Jupyter
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: scanpy >=1.6.0
Requires-Dist: anndata >=0.7.4
Requires-Dist: scHPL >=1.0.0
Requires-Dist: h5py >=2.10.0
Requires-Dist: torch >=1.8.0
Requires-Dist: numpy >=1.19.2
Requires-Dist: scipy >=1.5.2
Requires-Dist: scikit-learn >=0.23.2
Requires-Dist: matplotlib >=3.3.1
Requires-Dist: pandas >=1.1.2
Requires-Dist: scvi-tools >=0.12.1
Requires-Dist: tqdm >=4.56.0
Requires-Dist: requests
Requires-Dist: gdown
Requires-Dist: leidenalg
Requires-Dist: muon

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|PyPI| |PyPIDownloads| |Docs|


Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell data.


What is scArches?
-------------------------------
scArches allows your single-cell query data to be analyzed by integrating it into a reference atlas. By mapping your data into an integrated reference you can transfer cell-type annotation from reference to query, identify disease states by mapping to healthy atlas, and advanced applications such as imputing missing data modalities or spatial locations.


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

Support and contribute
-------------------------------
If you have a question or new architecture or a model that could be integrated into our pipeline, you can
post an `issue <https://github.com/theislab/scarches/issues/new>`__ or reach us by `email <mo.lotfollahi@gmail.com>`_.

Reference
-------------------------------
If scArches is helpful in your research, please consider citing the following `paper <https://www.nature.com/articles/s41587-021-01001-7>`_:
::


       @article{lotfollahi2021mapping,
         title={Mapping single-cell data to reference atlases by transfer learning},
         author={Lotfollahi, Mohammad and Naghipourfar, Mohsen and Luecken, Malte D and Khajavi,
         Matin and B{\"u}ttner, Maren and Wagenstetter, Marco and Avsec, {\v{Z}}iga and Gayoso,
         Adam and Yosef, Nir and Interlandi, Marta and others},
         journal={Nature Biotechnology},
         pages={1--10},
         year={2021},
         publisher={Nature Publishing Group}}




.. |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
