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: 1 day 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 (about 1 year ago)
• Default Branch: main
• Last Pushed: 2024-09-14T00:27:33.000Z (13 days ago)
• Last Synced: 2024-09-15T00:00:20.618Z (12 days ago)
• Language: Python
• Homepage:
• Size: 25.5 MB
• Stars: 84
• Watchers: 12
• Forks: 1
• Open Issues: 8
• 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.

Tutorials and API documentation can be found at:

https://genentech.github.io/scimilarity/index.html

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