PseudotimeDE for Differential expression of one gene in one lineage and two conditions

[dcruz5h]

Hello,

I am a little confuse. Can we use PseudotimeDE to test if the expression of a given gene differs between two conditions in one lineage ? or does PseudotimeDE only test if a given gene is differentially express along a given lineage ?

[SONGDONGYUAN1994]

Hi dcruz5h,
The current PseudotimeDE only tests if a given gene is differentially expressed along a given lineage. We do not include multi-lineage/condition cases because the pseudotime uncertainty is hard to summarize.

For your question, there are two methods (as far as I know) for testing multi-lineage+multi condition DE on pseudotimes:
condiments: https://hectorrdb.github.io/project/condiments/
lamian: https://winnie09.github.io/Wenpin_Hou/pages/Lamian.html

Best,
Dongyuan