Visium data analysis software supporting deconvolution analysis

Question

[Claire Watson]

Hi all,

Does anyone have recommendations for software that supports Visium data deconvolution analysis? Thank you in advance

[GenoMax]

This is likely a bleeding edge subject so things will be rapidly moving. I see the following

https://github.com/kpcoleman/SpaDecon
https://github.com/RubD/Giotto

A comprehensive list of 15 tools in table 1 of this paper: https://www.sciencedirect.com/science/article/pii/S200103702200558X

Answer 1

[jared.andrews07]

There are no shortage of these, including those that require a reference and reference-free options. I have never used any of them, so I have no recommendation.

STdeconvolve

Giotto

cell2location

SPOTlight

EnDecon

RCTD

Plenty more available via ye olde Google.

Answer 2

[jackson9]

I used BioTuring. They has good training models (this compapy started with scRNA, so they has lots of reference datasets). Cell2location is also implemented in the app.