MultiVI and Scenic+ cross-compatibility

[benduc]

Dear Scenic+ developers,
I recently found that MultiVI is a useful tool for batch correction of multiomic datasets. It uses "a deep generative model for probabilistic and integrative analysis of scRNA-seq, scATAC-seq and paired multi-modal data". I have a question about its compatibility with Scenic+:

• Can one use MultiVI for batch correction of multiomic datasets (10X Multiome for example) and run the batch-corrected output in Scenic+?
• If not, do you yourself recommend batch correction methods for multiomic datasets?

Thank you for all your work!

[SeppeDeWinter]

Hi @benduc

We usually don't do any batch effect correction before running SCENIC+

Best,

Seppe