README

This folder contains scripts used for scRNAseq analysis and associated figure generation for all the figures in our 2025 Science Immunology paper De novo thymus regeneration in a vertebrate, the axolotl.

Anna Czarkwiani†, Macrina Lobo†, Lizbeth Airais Bolaños Castro†, Andreas Petzold, Fabian Rost, René Maehr††, Maximina H. Yun††. De novo thymus regeneration in a vertebrate, the axolotl

†Equal contribution †† Corresponding authors

Required packages include:

• scanpy (and all associated libraries according to installation instructions )
• CellPhoneDB (and all associated libraries according to installation instructions )
• COMUNET (an R package for clustering and visualizing cell-cell interactions)