Tree-ensemble analysis assesses presence of multifurcations in single cell data.

We introduce TreeTop, an algorithm for single cell data analysis to identify and assign a branching score to branch points in biological processes which may have multi-level branching hierarchies. We demonstrate branch point identification for processes with varying topologies, including T-cell maturation, B-cell differentiation and hematopoiesis. Our analyses are consistent with recent experimental studies suggesting a shallower hierarchy of differentiation events in hematopoiesis, rather than the classical multi-level hierarchy.