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Hi @laurie-tonon, To correctly asses this you should plot the `stat` values instead of the `Log2FC` since this is what is used in the end to compute the enrichment score....

Hi @laurie-tonon, Yes, computing scores per sample and then comparing distributions is also a valid strategy. However, I would also expect few hits if the results contain so many non-significant...

Hi @AgentScientist, Pathway analysis can be performed at two levels: at the observation (cell) or contrast. In your case, you seem interested in the difference between conditions so first you...

Hi @AgentScientist, I would strongly advice against performing DEA at the single-cell level followed by enrichment analysis. Even if you have a balanced experimental design, still samples might contribute different...

Hi @sshanyiiii, It seems you are looking at an old vignette. To infer TF activities we have updated our tutorials, now we run TF activity inference through `decoupleR`, here's a...

Any updates on this feature? Currently I'm running stuff without a gpu because I cannot pass the `--nv` argument to my rules :/ I also tried to run with `snakemake...

Hi @simonvh and @Arts-of-coding , Thanks for the replies! It is really nice that it can be used using `AnnData`. I proposed `MuData` because its the extension of `AnnData` to...

Hi @jpfeil and @nierq, Indeed there seems to be a server side issue with the conversion. @deeenes could you take a look please?

Sorry to ask but are there any plans to fix this issue @crflynn? Unfortunately I will have to drop `skranger` as a dependency in if it is not supported for...

Hi @adamgayoso, Thanks for checking out the package! This seems like a problem coming from `omnipath`, that instead of returning gene names it returns protein ids from Uniprot. @deeenes could...