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Winnie09 / Lamian

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TDE and XDE tests with pseudotime data from other tools #7

Closed pchiang5 closed 1 year ago

pchiang5 commented 2 years ago

Hello,

Thank you for the tool.

Can I incorporate the outputs from other trajectory analyses into module 3 of Lamina?

For example, I have 2 trajectories (cluster 3 -> cluster 4 -> cluster 0 -> cluster 1 and cluster 3 -> cluster 4 -> cluster 2 -> cluster 5 -> cluster 7) with respective pseudotime data of from 1 sample. Is it reasonable to put the information into the 'design' parameter of the lamian.test() to compare the differential expression of the 2 trajectories?

xzsword commented 2 years ago

You can just turn the pseudotime into pseudotime rank and that will work. I checked the raw code and find the TSCAN pseudotime is the rank which is int. And it works for me (I used the slingshot)

Winnie09 commented 1 year ago

Thanks for helping answer the question, @xzsword! That will work. @pchiang5 In the online manual, I added a new section "Apply other pseudotime inference methods in Lamian: take slingshot as an example" : https://winnie09.github.io/Wenpin_Hou/pages/Lamian.html#apply-other-pseudotime-inference-methods-in-lamian-take-slingshot-as-an-example

Please feel free to let me know if you have other questions!