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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.


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

  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},
  publisher={Nature Publishing Group}}