work with multiple slices in SPATA2

theMILOlab / SPATA2

A Toolbox for Spatial Transcriptomics Analysis

https://themilolab.github.io/SPATA2/

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work with multiple slices in SPATA2 #134

Open sanrishiguang opened 4 months ago

sanrishiguang commented 4 months ago

In seurat, we can work with multiple slices as below:

How to work with multiple slices in SPATA2 ? And the step "denoising your data" should done before merging or after merging?

kueckelj commented 2 months ago

Hello sanrishiguang, if your goal is to horizontally integrate multiple Visium samples, I suggest you use Seurat. Currently SPATA2 does not inbuilt support for dealing with multiple slices in one object. What exactly is it, that you want to do? Furthermore, the autoencode functions are currently under supervision and will be exported again in upcoming version releases.