.. _pseudotime:

Pseudotime calculation
======================

To interpret the celloracle simulation results, it is important to compare the simulated cell identity shift vector with the direction of natural development.
We leverage pseudotime data to create development vector field.

.. warning:
   - The pseudotime analysis will be described in the future CellOracle paper.  This analysis is not included in our preprint.

   - Although we recommend doing pseudotime analysis to compare CellOracle simulation results with differentiation vector, you can skip this analysis if you just want to do bare minimum.


Please download the notebook from `here <https://github.com/morris-lab/CellOracle/blob/master/docs/notebooks/05_simulation/Pseudotime_calculation_with_Paul_etal_2015_data.ipynb>`_ .
Or please click below to view the content.

.. toctree::
   :maxdepth: 1

   ../notebooks/05_simulation/Pseudotime_calculation_with_Paul_etal_2015_data