bontix-77

error when running IdentifyOverExrpessedGenes

2

at the moment to run IdentifyOverexpressedGenes() i get: Error in `identifyOverExpressedGenes()`: ! Please check `[email protected]` and ensure that you have run `subsetData` and that the data matrix `[email protected]` looks OK....

netVisual issue

1

levels(cellchat@idents) + vertex.rece = rep(TRUE, 5)    + vertex.rece[1] = FALSE  + for (i in 1:length(pathways.show.all)) { +   netVisual(cellchat, signaling = pathways.show.all[i], vertex.receiver = vertex.rece, layout = "hierarchy") +   gg 

after convering in scanpy adata.uns['rank_genes_groups']['names'] contain numbers not gene names

2

i converted the SCT of a seurat object but then when i do the clustering by sc.tl.rank_genes_groups(adata, groupby='leiden', method='t-test') i get this : adata.uns['rank_genes_groups']['names'] rec.array([('2739', '14294', '11508', '14624', '4658', '11144',...