Daniel Dimitrov
Daniel Dimitrov
Hi @LJZYaaa, You would need to add CellChat as a method to RankAggregate in order to get it's output: See here: https://liana-py.readthedocs.io/en/latest/notebooks/basic_usage.html#Customizing-LIANA's-rank-aggregate Daniel
Hi @min0609, I am guessing here, but it's likely that the data that you've passed to liana is not normalised counts (which is the usual input that liana expects). So,...
Hi @LJZYaaa Yes, you must import those objects from liana - as done in a few lines above in the same tutorial. Daniel
Hi @npalacioescat, hmm no haven't - I will have a look soon
Hi @carlares, This might be better as an issue to the pyDESeq repo. Though, it seems like it might be simply the outlier filtering that they do. See a similar...
Hi @gianfilippo, An imported DEG should work just fine with liana :) Best wishes, Daniel
Hi @gianfilippo, I really suggest using the gurobi solver - it's likely that spicy's inbuilt one (HIGHs) is just resulting in very unstable results. @pablormier can maybe confirm or suggest...
Hi @pikapika505, I suggest making sure that the resource you use to define the network does not contain duplicates. Also, any edges in it are plausible to come up as...
Hi @and-rewsmith, Not sure if I understand the issue and let me know if I don't, but you get a lot of pvals of 0 because of the statistical test...
Hi @Bairea, Thanks, good catch. Will fix in next update. Daniel