Diffusion pseudotime robustly reconstructs lineage branching

Diffusion pseudotime (DPT) enables robust and scalable inference of cellular trajectories, branching events, metastable states and underlying gene dynamics from snapshot single-cell gene expression data. The temporal order of differentiating cells is intrinsically encoded in their single-cell expression profiles. We describe an efficient way to robustly estimate this order according to diffusion pseudotime (DPT), which measures transitions between cells using diffusion-like random walks. Our DPT software implementations make it possible to reconstruct the developmental progression of cells and identify transient or metastable states, branching decisions and differentiation endpoints.