kharchenkolab / thymus-mesenchyme

Code and notebooks for Gustafsson et al. scRNA-Seq analysis of thymic mesenchymal cells

Thymic mesenchymal niche cells drive T cell immune regeneration

Code and notebooks for Gustafsson et al. scRNA-Seq analysis of thymic mesenchymal cells. AnnData and conos objects are available from Zenodo repository (https://doi.org/10.5281/zenodo.6656930).

Content

• ipynb_notebooks contains .ipynb Jupyter notebooks:
  • 00_Data_preparation.ipynb: QC and creation of AnnData objects for the further analysis (view),
  • 01_Murine_thymus.ipynb: analysis of murine thymus composition (view),
  • 02_Human_thymus.ipynb: analysis of human thymus composition (view),
  • 03_Cross_species_alignment.ipynb: comparative analysis of murine and human thymic mesenchymal cells and validation of MC cell types on public data (view),
  • 04_Velocity_analysis.ipynb: RNA velocity analysis of Postn+ and Penk+ MCs from murine thymus (view),
  • 05_Bornstein_alignment.ipynb: validation of MC cell types on public data (view),
  • 06_Beta_regression.ipynb: some statistical computations (view),
  • 07_Figures.ipynb: figures preparation (view);
• tools contains additional functions that are used in Jupyter notebooks.