Jupyter notebooks for reproducing the results of Gupta et al. 2024.
The notebooks reproduce the preprocessing and annotation (01_annotation.ipynb), the trajectory analysis with Cytopath (02_cytopath.ipynb), and the exploratory trajectory analysis (04_cytopath_convergent.ipynb). Furthermore, the figures in the paper are reproduced in 99_figures.ipynb.
All AnnData objects used and created by the code in this repository, containing raw and processed expression data, are available on Zenodo at 10.5281/zenodo.10559456.