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. Synopsis TreeTop is a new algorithm that models single cell high‐dimensional data as an ensemble of trees to assess whether there is evidence of branching in the dataset. Branch point identification is validated on processes with varying and complex topologies. TreeTop gives a branching confidence score for single cell datasets to decide whether or not branching occurs. TreeTop is more specific than widely used alternative methods, which can suggest branches in data known to be non‐branching. TreeTop recapitulates branching and non‐branching structure in processes with known topologies, including T cell maturation, B cell differentiation and hematopoiesis. Our findings are consistent with recent studies suggesting a shallower rather than multi‐level hierarchy of differentiation events in hematopoiesis. Graphical Abstract TreeTop is a new algorithm that models single cell high‐dimensional data as an ensemble of trees to assess whether there is evidence of branching in the dataset. Branch point identification is validated on processes with varying and complex topologies.