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kstreet13 / slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
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one question about psuedo time inference #198

Closed YichaoOU closed 1 year ago

YichaoOU commented 2 years ago

Hi,

Does the algorithm have some weird behavior around the beginning or the end time point?

image

I'm not sure why 208 cells out of 4k cells all having 17.797586 as the pseudo time value. What parameters should I tune?

Thanks, Yichao

kstreet13 commented 2 years ago

Hi @YichaoOU ,

There are a couple different things that could be going on here, but it's hard to diagnose from this plot. Could you send a plot showing the dimensionality reduction you are using (including the curves produced by Slingshot) and the code you used to generate the curves, as well as the above plot? That should be enough to figure it out.

Best, Kelly