Hi @nmeo,
The genes presented by default in the Transcriptomics explorer manually curated based on the intersection of computational marker gene selection (using various methods) and literature search for biologically meaningful genes. These are by no means a complete set of marker genes, and there are many different ways to define them and it is hard to say which method is best. Here is an example review article. We often use scrattch.hicat or Seurat for our analysis pipelines, including marker gene definition, while Cytosplore uses a method that is less computationally intensive. I don’t understand what you mean by “cell-specific gene sets (rather than marker genes)”, but feel free to clarify if I didn’t already address it.
Best,
Jeremy