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kaishumason / NicheDE

NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.
https://kaishumason.github.io/NicheDE/
MIT License
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Deconvolved spatial data #6

Open elliewith opened 5 months ago

elliewith commented 5 months ago

Hello, is there deconvolved data available anywhere? Thanks!

kaishumason commented 5 months ago

Hello, Most spatial transcriptomic datasets do not come with a precomputed deconvolution. However, if you would like to use Niche-DE without deconvolution, some ST datasets that are single cell in resolution have cell type clusterings such as the MERFISH mouse brain from Moffit et al. (https://www.science.org/doi/10.1126/science.aau5324)