StemID is an algorithm for the inference of lineage trees and differentiation trajectories based on pseudo-temporal ordering of single-cell transcriptomes. It utilizies the clusters predicted by RaceID clustering tool.
In a nutshell, StemID infers links between clusters which are more populated with intermediate single-cell transcriptomes than expected by chance.
This will generate an RDS object, and a PDF showing a minimal spanning tree between the clusters, with the strength between clusters given by the colour and thickness of the branches.