Embedding cells and genes for post-training analysis takes a long time

[JunxiFeng]

Hi,

I was following the documentation to do the scRNA-seq analysis, but for the post-training analysis, it took a long time for me to embed the cells and the genes, is this normal? Or am I missing something here? Thank you so much!

[huidongchen]

Which particular step within the post-training analysis is experiencing a big delay?

If it is the UMAP step, unfortunately this is an unavoidable issue due to the extensive quantity of cells and features being visualized, and UMAP not being inherently the fastest.

A possible workaround is to visualize only cells with informative features, such as variable genes or top features based on SIMBA metrics.