Spatially Correlated Genes

scverse / squidpy

Spatial Single Cell Analysis in Python

https://squidpy.readthedocs.io/en/stable/

BSD 3-Clause "New" or "Revised" License

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Spatially Correlated Genes #910

Closed jamesboot closed 1 week ago

jamesboot commented 2 weeks ago

Sorry if I've missed this in the documentation, but is it possible to find spatially co-localised / correlate genes? I.e. gene A and gene B co-localise in space.

timtreis commented 1 week ago

Do you mean genes that show the same trends across the tissue?

jamesboot commented 1 week ago

Yes

timtreis commented 1 week ago

We do have this function: https://squidpy.readthedocs.io/en/stable/notebooks/examples/tools/compute_var_by_distance.html

However, I'm actually currently refactoring this to have better support for non-normalised distances 👍