Error when running Nichenet on spatial Seurat object about nichenetr

[browaeysrobin]

Hi @mvhunter1

This will indeed be the reason of the error and I can and will fix this easily and quickly.

I just have some questions concerning the direct application of NicheNet on 10x spatial transcriptomics data. In many cases, direct application won't be really appropriate I think. So, be sure it's ok to use NicheNet the way you are planning to do it. So this means: you should have changes in gene expression in receiver cells (in the spatial transcriptomics case 'spots containing multiple cells of the same of different cell types) caused by cell-cell interactions.
Feel free to ask me more questions about this if you would be in doubt.

I'll let you know when I fixed this problem.

[browaeysrobin]

Hi @mvhunter1

If you reinstall nichenetr now, you should be able to run the get_expressed_genes() and seurat wrapper functions on your spatial seurat object

[mvhunter1]

HI, thank you so much for your quick reply and fix. Yes, in my spatial transcriptomic data I have data from both tumor "spots" and spots from normal tissue surrounding the tumor. I'm looking to use Nichenet to examine communication between these two cell types. Thanks again for your help!