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3 hours ago by



I’m trying to run scVelo on my dataset but I’m running into some issues and was wondering if you could help me.

I have done my analysis on Seurat, and have subset and re-analysed sub-clusters and would like to run scVelo on those sub-clusters.
Im trying to run it following this pipeline :

The issue is I’ve stumbled on the first step. Is it possible to generate a loom file from Seurat that scVelo would accept and if so would you be able to give an example code of how? Trying the as.loom function in R on the subset Seurat object is being temperamental.
Velocyto has been very glitchy and since this is analysis on a subcluster I’m not sure how it would need to be run as the 10x files contain all the cells and I’m only interested in a subpopulation of those.

Thank you, and sorry for the naive question.


3 hours ago


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