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README.rst

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quickly and systematically leverage massive public scRNA-seq atlases to learn
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about a cell state of interest.
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Documentation
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Tutorials and API documentation can be found at:
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https://genentech.github.io/scimilarity/index.html
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Download
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Pretrained model weights, embeddings, kNN graphs, a single-cell metadata
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can be downloaded from:
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https://zenodo.org/records/10685499
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A docker container with SCimilarity preinstalled can be pulled from:
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https://ghcr.io/genentech/scimilarity
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Citation
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To cite SCimilarity in publications please use:
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**A cell atlas foundation model for scalable search of similar human cells.**
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*Graham Heimberg\*, Tony Kuo\*, Daryle J. DePianto, Tobias Heigl,
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Nathaniel Diamant, Omar Salem, Gabriele Scalia, Tommaso Biancalani,
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Jason R. Rock, Shannon J. Turley, Héctor Corrada Bravo, Josh Kaminker\*\*,
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Jason A. Vander Heiden\*\*, Aviv Regev\*\*.*
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Nature (2024). https://doi.org/10.1038/s41586-024-08411-y

docs/about.rst

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To cite SCimilarity in publications please use:
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**Scalable querying of human cell atlases via a foundational model reveals commonalities
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across fibrosis-associated macrophages.**
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Graham Heimberg\*, Tony Kuo\*, Daryle DePianto, Tobias Heigl, Nathaniel Diamant,
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Omar Salem, Gabriele Scalia, Tommaso Biancalani, Jason Rock, Shannon Turley,
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Héctor Corrada Bravo, Josh Kaminker\*\*, Jason A. Vander Heiden\*\*, Aviv Regev\*\*
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*bioRxiv.* `doi\:10.1101/2023.07.18.549537 <https://doi.org/10.1101/2023.07.18.549537>`__
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**A cell atlas foundation model for scalable search of similar human cells.**
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*Graham Heimberg\*, Tony Kuo\*, Daryle J. DePianto, Tobias Heigl,
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Nathaniel Diamant, Omar Salem, Gabriele Scalia, Tommaso Biancalani,
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Jason R. Rock, Shannon J. Turley, Héctor Corrada Bravo, Josh Kaminker\*\*,
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Jason A. Vander Heiden\*\*, Aviv Regev\*\*.*
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Nature (2024). https://doi.org/10.1038/s41586-024-08411-y

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