Error running nichenet_seuratobj_aggregate on v5 Seurat obj

saeyslab / nichenetr

NicheNet: predict active ligand-target links between interacting cells

452 stars 113 forks source link

Error running nichenet_seuratobj_aggregate on v5 Seurat obj #253

Closed DomenicoSkyWalker89 closed 2 months ago

DomenicoSkyWalker89 commented 4 months ago

Dear all,

while running nichenet analysis on my v5 seurat obj i got the following error:

Error in nichenet_seuratobj_aggregate(seurat_obj = FISM, receiver = "oligodendrocytes", :

no slot of name "data" for this object of class "Assay5"

Could you help me?

Best,

Domenico

csangara commented 4 months ago

Could you try following the step-by-step analysis instead and see if you can run the vignette? https://github.com/saeyslab/nichenetr/blob/master/vignettes/seurat_steps.md

In the meantime I'll try to fix the issue in the coming weeks.

niksa01 commented 4 months ago

I have this same issue, any update?

DomenicoSkyWalker89 commented 4 months ago

I followed the classical pipeline and it worked as always(as suggested by @csangara), so you can try with that.

csangara commented 3 months ago

I've implemented a fix for the wrapper functions now. Please update to v2.0.6 and let me know if there would be any issues. Note that the alias conversion function will not longer work for v5 objects.

avpatel18 commented 2 months ago

Hey! I have the same issue on V5 Seurat object with nichenetr V2.0.6 version. It seems like you have fixed this two weeks ago but not sure why I am still getting error. Any help much appreciated!

csangara commented 2 months ago

@avpatel18 Is it the same error as above? Could you also provide your sessionInfo()?

avpatel18 commented 2 months ago

@csangara thank you for getting back to me. I had some other dependency issue but after fixing that all working now.