Hi!
I am integrating different single-cell atlases and testing different methods like scVI and scANVI and then benchamrking them using scib-metrics package to assess the quality of the integration. However, I also wanted to integrate the newly developed mthod called CellHint Google Colab. However CellHint calculated the new corrected distances and connectivies that are then used to draw the new batch corrected umap. I was wondering if I can use the CellHint umap embedding in embedding_obsm_keys and compare them to the scVI and scANVI embeddings. Thank you for your help!
This is the general way to perform the comparison. scib-metrics does not work with precomputed neighborhood graphs and requires an embedding.