https://github.com/genentech/scimilarity
A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training.
https://github.com/genentech/scimilarity
Last synced: about 1 year ago
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A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training.
- Host: GitHub
- URL: https://github.com/genentech/scimilarity
- Owner: Genentech
- License: other
- Created: 2023-08-08T03:15:35.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2025-05-06T22:54:23.000Z (about 1 year ago)
- Last Synced: 2025-05-06T23:28:36.311Z (about 1 year ago)
- Language: Python
- Homepage: https://genentech.github.io/scimilarity/
- Size: 25.5 MB
- Stars: 187
- Watchers: 11
- Forks: 7
- Open Issues: 22
-
Metadata Files:
- Readme: README.rst
- Changelog: NEWS.rst
- License: LICENSE
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README
SCimilarity
================================================================================
**SCimilarity** is a unifying representation of single cell expression profiles
that quantifies similarity between expression states and generalizes to
represent new studies without additional training.
This enables a novel cell search capability, which sifts through millions of
profiles to find cells similar to a query cell state and allows researchers to
quickly and systematically leverage massive public scRNA-seq atlases to learn
about a cell state of interest.
Documentation
--------------------------------------------------------------------------------
Tutorials and API documentation can be found at:
https://genentech.github.io/scimilarity/index.html
Download & Install
--------------------------------------------------------------------------------
The latest API release can be installed from PyPI::
pip install scimilarity
Pretrained model weights, embeddings, kNN graphs, a single-cell metadata
can be downloaded from:
https://zenodo.org/records/10685499
A docker container with SCimilarity preinstalled can be pulled from:
https://ghcr.io/genentech/scimilarity
Citation
--------------------------------------------------------------------------------
To cite SCimilarity in publications please use:
**A cell atlas foundation model for scalable search of similar human cells.**
*Graham Heimberg\*, Tony Kuo\*, Daryle J. DePianto, Tobias Heigl,
Nathaniel Diamant, Omar Salem, Gabriele Scalia, Tommaso Biancalani,
Jason R. Rock, Shannon J. Turley, Héctor Corrada Bravo, Josh Kaminker\*\*,
Jason A. Vander Heiden\*\*, Aviv Regev\*\*.*
Nature (2024). https://doi.org/10.1038/s41586-024-08411-y