Dear development team,
First, thanks a lot for this wonderful package! This tool is very useful and we plan to use it to integrate an Atlas. However, we have a significant batch effect and we are not completely satisfied with scVI.
I have seen that scVI recently made a new model called sysVI specifically for this kind of analysis. (https://docs.scvi-tools.org/en/latest/user_guide/models/sysvi.html)
Do you plan by any chance to integrate it on your tool? We very much like to use the functionality to share the model and the ability to transfer the model with the discovery of new cell types in the query dataset.
Best