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HectorRDB / condiments

Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
https://hectorrdb.github.io/condiments/
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How to handle cells that belong to multiple overlapping lineages #9

Closed jeremymsimon closed 2 years ago

jeremymsimon commented 2 years ago

Hey @HectorRDB - my slingshot trajectories look like this:

Screen Shot 2021-10-28 at 9 14 51 AM

where cells in the green clusters actually belong to all 3 lineages detected by slingshot. There are two conditions, as depicted by the different shading of each color.

In each of the example datasets I've seen for condiments, cells belong to one and only one lineage, and it isn't clear how to set everything up in cases such as mine. Can you provide some guidance on that?

HectorRDB commented 2 years ago

HI @jeremymsimon Thanks for asking. First, you can refer to the KRAS analysis vignette from the package that accompagnies our paper.

You can run the topologyTest and then the progressionTest and fateSelectionTest without issues when hyou have more than 1 lineage, the code should be quite similar. Let me know if you encounter any problems. Best

jeremymsimon commented 2 years ago

Ah yes I see, thanks! Will model after that