Single cell RNA-seq allows us to profile the diversity of cells along a developmental time-course. However, we cannot directly observe cellular trajectories because the measurement process is destructive. Waddington-OT is designed to infer the temporal couplings of a developmental stochastic process from samples collected independently at various time-points. The temporal couplings tell us what descendants cell $x$ from time $t_i$ would give rise to at time $t_j$


A practical, hands-on introduction to inferring trajectories with wot.

Command Line

A command line interface that offers fine-grained control over all calculations.

wot optimal_transport


Type pip install wot in your terminal to install wot and all required dependencies. Please note that Python 3 is required.

Source Code

The full source code is available on Github.