Chananchida Sang-aram

Hi, It seems like the error is occurring in one of the visualizations, i.e., the creation of the LFC plot. I would suggest that you follow the [step-by-step vignette](https://github.com/saeyslab/nichenetr/blob/master/vignettes/seurat_steps.md) instead...

Hi, From NicheNet v2 onwards we started using nsga2R optimization instead of mlrMBO, as it is much faster. Unfortunately this means I am not able to help you with this...

Hi Theo, The optimization step can slightly improve the performance of NicheNet target gene prediction but I would not say it is very critical (see [Supplementary Notes Figure 2.3 and...

Dag Smeerlap, 1. Finn is correct that the ligands are in the columns and target genes are in the rows. An easy way to check is by using `dim` and...

Hi, Can both of you check that your NicheNet version is 2.1.5? This issue should have been fixed in #198, but it's possible that I overlooked some lines of code.

I still can't figure out what's going wrong here. If anyone could provide me with the following, it will be very helpful. - Their `sessionInfo()` - The version of their...

Indeed, you'll either have to break it into pairwise comparisons or perform a one vs two DE analysis to define the gene set of interest. If you have multiple samples...

Hi, two things you could try: 1) Check whether there was a typo in the argument (i.e., has to be `recorrect_umi = F` instead of `reccorect_umi= F`) 2) Check if...

Hi, Thanks for you interest in our tool. NicheNet can be used on bulk data of sorted cell populations by storing your data in another format -- e.g., a normal...

Thanks for using our package! I'd first like to ask some clarifications on your issue, as the function you are running comes before the one referenced in issue #220. Let...