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carmonalab / GeneNMF

Methods to discover gene programs on single-cell data
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NMF for spatial transcriptomics ? #15

Open gabriel-pozo opened 3 weeks ago

gabriel-pozo commented 3 weeks ago

Hi! Thanks for the great tool! Could GeneNMF be applied to 10x visium data ?

mass-a commented 3 weeks ago

Hey Gabriel, we have not tested the tool on Visium data, but in principle it should work! Although it would lack single-cell resolution and perhaps pick up spurious signal from mixed spots, you may be able to learn broad gene programs and link them to their spatial location. I would be interested in seeing what results you get.

Cheers -m

gabriel-pozo commented 3 weeks ago

Thanks! I'll run and share the results later. Kind regards