search

bhuvad / SpaNorm

R package for normalisation of spatial transcriptomics data
https://bhuvad.github.io/SpaNorm/
GNU General Public License v3.0
9 stars 1 forks source link

Compatibility with Seurat objects #3

Open ashsolano opened 1 month ago

ashsolano commented 1 month ago

Hi, I had a read of you preprint and think that SpaNorm looks like a great tool to test on some MERSCOPE and Xenium data I am currently analyzing. I was wondering whether the SpaNorm package can work directly on Seurat objects or is only SpatialExperiment Object compatible? Also, will an example of image based technique such as Xenium become available in the documentation which currently only has 10x Visium DLPFC of the human brain? Thanks

bhuvad commented 1 month ago

Hi @ashsolano,

Making SpaNorm work on Seurat objects is on my to-do list and I have accounted for this use case so if all goes well, it should be available soon. That said, Seurat objects are a bit tricky to work with so it could be longer. In the meantime, you could convert the Seurat object into a SpatialExperiment object (as(seurat_object, "SpatialExperiment")), run SpaNorm, and then convert back using Seurat::as.Seurat(spe_object). I think the current transformation functions cannot handle coordinates so you may need to copy over coordinates to and from your Seurat objects.

I will try my best to get the function compatible for Seurat objects, however, I cannot at this point provide an exact timeline of when implement this feature.

Cheers, Dharmesh