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
Release files for scimilarity 0.4.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| scimilarity-0.4.1.tar.gz | 10.3 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scimilarity-0.4.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 10.4 MB
Release files / scimilarity-0.4.1.tar.gz
| Download URL | scimilarity-0.4.1.tar.gz |
|---|---|
| Size | 10.3 MB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.12.10
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Release files / scimilarity-0.4.1-py3-none-any.whl
| Download URL | scimilarity-0.4.1-py3-none-any.whl |
|---|---|
| Size | 60.2 kB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.12.10
|
