Can I using scVI to integrate data, then using R to conduct following analysis?

Question

[Andy]

Hello everyone,

I am wondering if I could use Python to integrate my data and then use R to conduct downstream analysis, such as CellChat, etc.

Thank you,
Andy

Answer 1

[bk11]

Can you please tell us what type of data are you planning to integrate? You can also use scVI to integrate single cell data in R using Seurat package. You need is scVI-environment in conda.

       Seurat_object <- IntegrateLayers(
      object = Seurat_object, method = scVIIntegration,
      new.reduction = "integrated.scVI",
      conda_env = "../miniconda3/envs/scvi-env", verbose = FALSE
    )

https://satijalab.org/seurat/articles/seurat5_integration

[Andy]

Thank you. But my data is huge. This is why I use python. After integration I want to use R for the further analysis. Thanks for your sharing.

Answer 2

[fracarb8]

There is an entire section on scVI documentation about running it through reticulate.