I wonder if someone could please advise on two points in the scanpy guidance for CITEseq analysis please.
When clustering protein and RNA together it suggests using sc.tl.leiden_multiplex, however I get this error: AttributeError: module ‘scanpy.tools’ has no attribute ‘leiden_multiplex’ … I cannot find leiden_multiplex on the sc.tl documents … does it exist?
On line 36 it performs pbmc.X[:, (pbmc.var[“feature_types”] == “Gene Expression”).values] = rna.X … however i get a shape mismatch (ValueError: shape mismatch in assignment), despite following the steps meticulously. I’m wondering whether the RNA filtering steps (which are part of the tutorial) maybe caused this? Has anyone else come across this?