Introduction

This repository contains code for reproducing the figures and results in the paper Trajectory inference from single-cell genomics data with a process time model by Meichen Fang, Gennady Gorin, Lior Pachter, PLoS Computational Biology, 2025.

Repository Contents

• Chronocell/: The Python package that implements the fitting procedures. The code for the package is maintained in a separate repository https://github.com/pachterlab/Chronocell. This repository contains a copy of the version of the code used for the paper for completeness.

• simulations/: Notebooks to perform analyses on simulations.

• notebooks/: Notebooks to perform analyses on biological datasets.

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