A technical question,
I was to further study the diversity within certain clusters in my dataset,
So far, I would usually subset, calculate the HVG and then re-integrate them and run the UMAP.
The results seem fine but I just want to know if this would be a good practice or if I am doing something wrong.
I am working with Seurat and SCVI in R
Seems like fine. That’s how I do it typically but in scanpy
Honestly, Sometimes I regret that I started with R as it is harder for me know to learn Python allover again