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kstreet13 / slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
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how to justify lineages inferred by slingshoot? #164

Closed FADHLyemen closed 2 years ago

FADHLyemen commented 2 years ago

Hi, Slingshoot inferred two lineages, how to justify why we have two lineages? any ideas?

kstreet13 commented 2 years ago

I think that is largely an issue of biological interpretation. I would recommend trying to assign known cell types to the endpoints to see if they make sense, or examining the behavior of established marker genes to see if their patterns of expression are consistent with your expectations.

FADHLyemen commented 2 years ago

@kstreet13 When I use pca in slingshot function, 1 lineage was predicted, when I use umap, slingshot inferred two lineages. which one is correct?

kstreet13 commented 2 years ago

Please do not post the same question multiple times.

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