Export the neighbor graph from integrated Seurat objective and import to scvelo

theislab / scvelo

RNA Velocity generalized through dynamical modeling

https://scvelo.org

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Export the neighbor graph from integrated Seurat objective and import to scvelo #1245

Closed Alvis-Jiang closed 1 month ago

Alvis-Jiang commented 2 months ago

Hi,

I have an integrated Seurat objective with SCT, and I want to use the precomputed PCA, UMAP and neighbor graph for scvelo. Could you give me some guidance on what content of neighbor graph should I export from seurat?And the neighbor of scanpy includes "distance" and "connectiveness", I assumed that snn graph could be the connectiveness, but what should I export from seurat as "distance" in the anndata?

Thank you so much!