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


Pip installation

Note that due to a limitation of pip, cython and numpy need to be installed prior to installing wot using the command:
pip install numpy cython
You can then install wot with:
pip install wot

Anaconda installation

Install pot dependency:
conda install -c conda-forge pot
Install wot (and additional dependencies):
pip install wot

Source Code

The full source code is available on Github.