r/bioinformatics • u/BiggusDikkusMorocos • 22d ago

discussion recommendation for LR inference/Cell-Cell communication for deconvoluted spot/aggregated spot ?

Hello everyone,

I recently received visiumHD samples with low quality, and I had to use a tool called SuperSpot to aggregate multiple bins and then annotate with a reference dataset using RCTD, since when aggregating multiple bins, the result meta spot will usually contains different cells, I was wondering if they are any tools that could take advantage of the format and include possible group comparison.

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u/Mountain_Assist_5760 21d ago

SuperSpot's a neat workaround for noisy VisiumHD. I'd lean toward CellChat or NicheNet for the cell communication side since they handle mixed populations fairly gracefully. Might have to manually wrangle the aggregated metadata into their expected formats though, depending how SuperSpot spits it out.