What would be the most straightforward way to change gene names in the AnnData object?
You can just do the following:
adata.var_names = new_gene_names_in_correct_order
The second list can be created by, e.g.:
new_gene_names_in_correct_order = ['newName' if id=='gene A' else id for id in adata.var_names]
Great, thanks a lot!