Jupyter notebooks for reproducing the results of Schleicher et al. 2025.
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.
@article{10.1371/journal.pone.0332406,
doi = {10.1371/journal.pone.0332406},
author = {Schleicher, Jan T. AND Gupta, Revant AND Cerletti, Dario AND Sandu, Ioana AND Oxenius, Annette AND Claassen, Manfred},
journal = {PLOS ONE},
publisher = {Public Library of Science},
title = {Exploratory trajectory inference reveals convergent lineages for CD8 T cells in chronic LCMV infection},
year = {2025},
month = {09},
volume = {20},
url = {https://doi.org/10.1371/journal.pone.0332406},
pages = {1-25},
number = {9},
}