/FGP_2024

Primary LanguageJupyter Notebook

Introduction

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

Repository Contents

  • 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