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Visium deconvolution reference datasets

I am investigating some methods for Visium deconvolution. Looked at some benchmark papers and most of the top accurate algorithms relied heavily on reference datasets.

So can anyone suggest me source to find trustable - datasets? I tried to explore cellxgene but seem like their metadata is messy and not consistent.

visium-deconvolution spatial
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updated by jackson9 • jackson9 • written by Claire Watson • Claire Watson

2 answers

Oh Great! Thank you so much. I'll definitely check it out!

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written by Claire Watson • Claire Watson

True, it's the reference dataset that determine result of deconvolution, not the algorithm.

A good reference datasets depend on lots of factors such as tissue, condition, cell types, unit... related to your visium dataset. So you have to filter out yourself, unfortunately.

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written by jackson9 • jackson9

It's worth to take a look at BioTuring. This company is well-known with its standardized metadata, so I think they have lots of good reference scRNA datasets there.

They also implemented cell2location in their app. You can book a demo to see how it works

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written by jackson9 • jackson9

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