Another point confused me is what you mentioned in your tutorial and your paper(congrats!), you think there are some apoptosis pathway related genes enrich in cluster2, how do you define it ? Is there any way to determine it automatically?
We used the enrichment tool provided by the Gene Ontology Consortium as a part of our analysis. This really requires someone knowledgable in cellular processes and pathways to evaluate the significance of the results, so it is best done manually. Tools to run this will be available in a package we are presently working on (scGPS).
As requested by @MichaelPeibo in #14:
We used the enrichment tool provided by the Gene Ontology Consortium as a part of our analysis. This really requires someone knowledgable in cellular processes and pathways to evaluate the significance of the results, so it is best done manually. Tools to run this will be available in a package we are presently working on (scGPS).