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dynverse / dyno

Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
https://dynverse.github.io/dyno
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Anyone have more information about PAGA Tree? #89

Open jpcartailler opened 4 years ago

jpcartailler commented 4 years ago

I can't seem to find any independent information (paper, repository, docs, nothing at all) that describes PAGA Tree. Is it some special configuration of PAGA? We've having good success with PAGA Tree, but would like to read more about it... hopefully someone can point me in the right direction, or point out what might be in front of my face. Cheers!

Edit: After some more digging around, I think the only difference between PAGA and PAGA Tree is that PAGA has a connectivity_cutoff (https://github.com/dynverse/ti_paga/blob/master/definition.yml). So, if the method was run standalone without the connectivity_cutoff, then would it yield the same output as PAGA Tree?

Bio-data-tricks commented 3 years ago

Hello c5creative,

Did you get the answer to your question? It seems that PAGA tree doesn't require any prior information like start_id.

Nicolas

soheilj commented 1 year ago

I'm not a member of dynverse nor paga teams but this is what it says in ti_paga_tree documentation in dynverse.

Will generate a trajectory using PAGA Tree. This method runs exactly the same as normal PAGA, but will construct a minimal-spanning tree between clusters