theislab/scarches
Reference mapping for single-cell genomics
This tool helps single-cell biologists analyze new single-cell genomics data by integrating it into existing, well-annotated reference atlases. You input your raw single-cell data, and it outputs analyzed data with cell-type annotations, disease state identifications, or even imputed missing data. This is for researchers and scientists working with single-cell genomics.
400 stars. Available on PyPI.
Use this if you need to rapidly annotate cell types in new single-cell datasets, identify disease-associated cell states, or leverage comprehensive reference atlases to understand your query data.
Not ideal if you are looking to build a reference atlas from scratch or if your research does not involve mapping new data to existing references.
Stars
400
Forks
70
Language
Jupyter Notebook
License
BSD-3-Clause
Category
Last pushed
Dec 02, 2025
Commits (30d)
0
Dependencies
16
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