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prabhakarlab / Banksy

BANKSY: spatial clustering
https://prabhakarlab.github.io/Banksy
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Multi sample analysis on seurat object #25

Closed alirezaah98 closed 6 months ago

alirezaah98 commented 7 months ago

Hello there,

I have been using BANKSY for each sample separately on Xenium data but I was wondering if there was a way to do the multisample analysis on seurat object as well or not? by converting it to Spatialexperiment object, it completely ruins the spatial plot and all the clusters we get, are distorted and don't show any spatial pattern , at all. Thanks

jleechung commented 7 months ago

Hi @alirezaah98, we've just implemented multi-sample analysis for Seurat. Please reinstall with

remotes::install_github('jleechung/seurat-wrappers@feat-aft')

and see here for how to run multi-sample analysis. I'm not sure if switching from SpatialExperiment to Seurat will solve your issue however. If you can share your analysis code and sessionInfo that would be helpful

vipulsinghal02 commented 6 months ago

Closing this for now. @alirezaah98 feel free to reopen it if if you still need help (and would like to share your code / sessioninfo).