Dear all,

i am following the tutorials on SEURAT3 wrappers and HARMONY, LIGER, CONOS, etc, as these are presented at :

https://htmlpreview.github.io/?https://github.com/satijalab/seurat.wrappers/blob/master/docs/liger.html https://htmlpreview.github.io/?https://github.com/satijalab/seurat.wrappers/blob/master/docs/conos.html

and I am using the commands on our laboratory scRNA-seq datasets. If my understanding is correct, after we process the data according to the methods that are presented in the tutorials,

we shall follow the tutorial : https://satijalab.org/seurat/v3.1/immune_alignment.html, in order to learn cell specific responses :

-- Identify conserved cell type markers : FindConservedMarkers

-- Identify differential expressed genes across conditions : FindMarkers

thanks,

bogdan

ps : 've posted the question also on SEURAT github : https://github.com/satijalab/seurat/issues/2667