Notebook 05: Filter marker gene lists on based on genes present in the dataset
When giving a list of marker genes which are not present in the dataset some functions called in notebook 5 do not account for that (scanpy.umap, marker_gene_clustering,..).
The easiest option would be add a cell that filters the marker gene lists:
for key, genes in marker_genes_dict.items():
marker_genes_dict[key] = [g for g in genes if g in adata.var.index]
print(f"Reomved {[g for g in genes if g not in adata.var.index]} from {key} marker gene list")