Can SpatialGlue support integrate multiple replicates of RNA+ATAC multiomics slices?

[EddieLv]

I have 3 replicates of spatial RNA+ATAC multiomics data, can SpatialGlue integrate them together? Or I must cluster each slice individually?

[longyahui]

Hi,

Thank you for your attenion on wor work.

The current version of our SpatialGlue only supports single slice input. You can combine these 3 replicates of spatial RNA+ATAC before input of the model, and then analyze the combined sample using SpatialGlue.

Hope it helps. Thanks again.

Best regards,
Yahui

[EddieLv]

@longyahui Hello, glad to use this fantastic tool!
As you said, I can combine these 3 replicates as one input for the model (only when there are small batch effects across replicates). While I still have a question:
1.If the batch effect is quite strong, can I use integration-tools such as [harmony] to integrate the co-embeddings of each replicate of SpatialGlue? Does it make sense?
Best wishes!