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genepattern / Tangram

A method for mapping sc/snRNA-seq data to various forms of spatial data collected from the same region.
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Test input/output ... #4

Closed edwin5588 closed 3 weeks ago

edwin5588 commented 5 months ago

... and see if it matches example notebook outputs

omarhalawa3301 commented 4 months ago

Achieves same output as the "with_squidpy" notebook (excluding the Deconvolution cells). Should match the "without_squidpy" version (excluding crossval functionality) but might have some issues due to that notebook using older code and dependencies.

jkononova3 commented 4 months ago

Leaving this issue open for now, would like to test with additional input datasets (referred to by Tangram developers) before closing.

omarhalawa3301 commented 4 months ago

This dataset might be worth considering. Also need to validate the "without_squidpy" notebook.