Alexey Sergushichev

Also, probably, `amount` string should be used in the file name. Otherwise, the caching will be incorrect, when you first download, say, "quick" and then "full" file.

I would expect some difference due to randomness of the algorithms. You should get similar difference between different runs of the same algorithm. You'd better compare p-values of the same...

Can you please provide a reproducible example?

Thanks for the example. Indeed there is a bug in incorrect handling of NA in gene names. As a workaround you can apply `gene_list

@G3N0M3 apparently, package reinstallation has helped some of the people with the same problem: https://github.com/YuLab-SMU/clusterProfiler/issues/568 But as you said you did it already, as a workaround I can suggest to...

> NA values make me think that the enrichment may not be that strong to start with, but with the higher nPermSimple, now it is highly significant. No, `NA` values...

@chriswzou fgsea results are supposed to be reproducible, so this looks like a bug. However, we would need more info from you. Specifically, can you provide a minimal example with...

@macsennett your example works as it is supposed to work: it is reproducible, that is you can run the same code again and will get the same `sig.pvals` vector. You...

@Pedramto89 I've pushed some updates to the plotting code and the vignette. Please, check it out (you need to install the package from github with `devtools::install_github('ctlab/fgsea')`), may be it will...

@Pedramto89 try to use the new `plotCoregulationProfileSpatial` as in here: https://github.com/ctlab/fgsea/blob/master/vignettes/geseca-tutorial.Rmd The values there are z-scores of the average gene expression of the gene set. The titles can be shortened...