Single-cell gene expression profiles of differentiating cells encode their intrinsic latent temporal order. We describe an efficient way to robustly estimate this order according to a diffusion pseudotime , which measures transitions on all length scales between cells using diffusion-like random walks. This allows us to identify cells that undergo branching decisions or are in metastable states, and thereby genes differentially regulated at these states.

Diffusion pseudotime robustly reconstructs lineage branching