https://github.com/theislab/scarches

Reference mapping for single-cell genomics
https://github.com/theislab/scarches

batch-correction data-integration deep-learning human-cell-atlas multimodal-deep-learning multiomics rna-seq-analysis scrna-seq single-cell single-cell-genomics

Last synced: 3 days ago
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Reference mapping for single-cell genomics

• Host: GitHub
• URL: https://github.com/theislab/scarches
• Owner: theislab
• License: bsd-3-clause
• Created: 2019-08-12T19:51:11.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2025-05-22T12:21:13.000Z (5 months ago)
• Last Synced: 2025-05-22T14:06:36.537Z (5 months ago)
• Topics: batch-correction, data-integration, deep-learning, human-cell-atlas, multimodal-deep-learning, multiomics, rna-seq-analysis, scrna-seq, single-cell, single-cell-genomics
• Language: Jupyter Notebook
• Homepage: https://docs.scarches.org/en/latest/
• Size: 825 MB
• Stars: 365
• Watchers: 11
• Forks: 59
• Open Issues: 59
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

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• StarryDivineSky - heislab/scarches - seq) 参考图集并共享经过训练的模型和数据（如果可能）。为您感兴趣的地图集下载预先训练的模型，使用新数据集对其进行更新并与您的合作者分享。在参考的顶部投影和集成查询数据集，并使用潜在表示进行下游任务，例如：差异测试、聚类、分类 (其他_生物医药 / 网络服务_其他)

README

          
.. raw:: html

 

|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 `_ 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 `__ or reach us by `email `_.

Reference

-------------------------------

If scArches is helpful in your research, please consider citing the following `paper `_:

::

       @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