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Recommended minimum number of cells to run PHATE? #127

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kuang-da opened this issue Jan 29, 2023 · 0 comments
Open

Recommended minimum number of cells to run PHATE? #127

kuang-da opened this issue Jan 29, 2023 · 0 comments
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@kuang-da
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Hi,

Thank you very much for the great dimension reduction method! I am working on a cell differentiation project and thinking about trying PHATE, but the only concern is that I have ~180 cells with relatively deep sequencing depth (~5M reads per cell). Do you feel PHATE could be applied to my dataset with a limited number of cells? Is there any heuristic recommendation about the minimum number of cells to run PHATE based on your lab's expertise and experience?

Thank you!

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