ImmuneDeconv with spatial transcriptomic data #183
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SoniaHermoso
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Hello Sonia, spacedeconv would be the perfect solution for you as it supports both immunedeconv and omnideconv: https://github.com/omnideconv/spacedeconv |
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Hello!
I have spatial transcriptomic (ST) data from Visium and I would like to use immunedeconv package with it. Specifically, the methods xcell and CIBERSORT.
My question is about the input data. For example, I have my ST data in a Seurat object. After to normalize with SCTransform() function, I have 3 types of data: "counts", "data" and "scale.data". I think that the best option to use in immunedeconv is the "data" type, but I am not sure.
Could anyone help me and to say if this is correct or, if not, how I have to transform my data to use it in ImmuneDeconv , please?
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