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Question about clustering optimization + nearest neighbor graph extraction #11

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JahanRahman opened this issue Nov 15, 2024 · 0 comments

JahanRahman commented Nov 15, 2024

Hello,

Thank you so much for your very helpful tool. I just had a few quick questions:

How does scINSIGHT determine which clustering resolution to use when running the Louvain algorithm?
If we wanted to run our own clustering (ie using leiden), is it possible to somehow extract the nearest neighbor graph generated by scINSIGHT? Or is it advisable to use the normalized common module matrix to run nearest neighbor detection on our own (ie using FindNeighbors in Seurat)?

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