This repository contains code for reproducing the figures and results in the preprint Meichen Fang, Gennady Gorin, Lior Pachter (2024).

• Chronocell/: a python package that implement the fitting

  • inference.py: contains the Trajectory class and methods for fitting.
  • mixtures.py: contains the code and classes for Poisson mixture model.
  • models/: contains the model specific functions to calculate log likelihood and optimize parameters.
  • simulation.py: contains the code for generating simulations.
  • plotting.py: contains some convenient but not essential functions for plotting.
  • utils.py: contains some helper functions.

• simulations/: notebooks to perform analyses on simulations.

• notebooks/: notebooks to perform analyses on real datasets.

  • forebrain.ipynb
  • erythroid.ipynb
  • rpe1.ipynb
  • PBMC.ipynb
  • Neuron.ipynb