Robin Browaeys
Robin Browaeys
Hi @mimisikai What would you expect/want to be different than the vignette currently presented by the developers of LIANA? We don't have time to work on this the next couple...
Hi @mimisikai You could indeed use LIANA's output to replace the entire lr_network of NicheNet. You can also check the cell-cell communication tutorial from this github page https://github.com/saezlab/eccb2022_sc_funcomics - here...
Hi @DzenisKoca Sorry for the late reply. I would guess this is correct, but I think the Seurat developers would be more qualified to answer this question. Could you ask...
Hi @anaccsilva We will solve this around the 18th of November
Hi @ejc043 > From what I understand, the workflow of ranking putative ligands is to rank ligands based on how predictive they are for downstream genes. This is indeed true...
Hi @annamath Do you mean that you want to have a score per senderLigand - receiverReceptor pair that includes both cell-type specific expression and NicheNet ligand activity? Or do you...
Hi @annamath Do you want to include the cell type information at the ligand-target level or at the ligand-receptor level? Or both? Based on your first message and your reference...
Hi @Zethson I will have a look into this.
@ejc043 Because of multiple projects and lack of time, this is currently not one of my main priorities (this can change if you can convince me that adding it to...
Hi @chrismahony This is an error that sometimes can occur when one of the label names is duplicated (probably there might be other reasons also...). In the context of the...