as I have just started reading the documentation on SEURAT for scRNA-seq (among a few other packages), I would appreciate having your answers and insights please on the following :
after NormalizeData() function, why ScaleData() function is needed ?
is FindVariableGenes() or RunPCA() or FindCluster() working on Normalized_Data or on Scaled_Data ?
is ScaleData() working on RAW_DATA or on NORMALIZED_DATA ?
is RunCCA() working on Normalized_Data or on Scaled_Data ?
an example of R code is at : https://satijalab.org/seurat/immune_alignment.html
thanks a lot !