Run bbknn followed by leiden clustering and run umap on the result.

Run harmony integration followed by neighbour calculations, leiden clustering and run umap on the result.

Run scanorama integration followed by neighbour calculations, leiden clustering and run umap on the result.

Run scvi integration followed by neighbour calculations, leiden clustering and run umap on the result.

Run totalVI integration, followed by neighbour calculations, leiden clustering and UMAP.

Run totalVI integration by mapping the query dataset to a reference, followed by neighbour calculations, leiden clustering and run umap on the result.