search

prabhakarlab / Banksy

BANKSY: spatial clustering
https://prabhakarlab.github.io/Banksy
Other
74 stars 12 forks source link

Double the features in BANKSY assay in seurat object #23

Closed alirezaah98 closed 7 months ago

alirezaah98 commented 8 months ago

Hello,

I have been running the banksy on seurat object and we have a limited number of features in the dataset , we chose to run it on all the features. After running the algorithm , it doubles the features with adding ".m0" to each gene name and also it makes to be repeated in the downstream with finding marker genes. It would be great if you could explain why this thing heppens?

Thanks

jleechung commented 8 months ago

Hi @alirezaah98, BANKSY uses a feature augmentation approach for capturing spatial information. The additional features m0 correspond to the mean expression in the local neighbourhood - see Figure 1a of the paper.

To find markers within the original gene set after running BANKSY clustering, set the default assay to RNA before running FindMarkers - see the vignette here please.