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Caochris / SCOTIA

MIT License
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Short description of method #9

Closed lgeistlinger closed 5 months ago

lgeistlinger commented 8 months ago

It would be helpful to provide a three-sentence summary paragraph of the method right in the beginning of the README.

Currently it says:

"Scotia is a Python package for inferring ligand–receptor interactions from spatial imaging data."

This could be expanded.

Eg:

"Spatially Constrained Optimal Transport Interaction Analysis (SCOTIA) is a Python package for inferring cell-cell interactions from imaging-based spatial omics data. The main idea of the method is to use an optimal transport model with a cost function that includes both spatial distance and ligand–receptor gene expression. The three key steps of the method are: (1) spatial clustering to identify adjacent source and target cluster pairs, (2) scoring of candidate cell-cell interactions by solving an optimal transport problem between spatially proximal source and target cluster, and (3) significance assessment of the resulting spatially-constrained cell-cell interaction scores through permutation."

Also linking to the preprint at the end of the summary paragraph would be helpful for anyone wanting to reading up on the details.

Caochris commented 7 months ago

Thanks for your suggestions! I added the description and citation.