In this repository you will find all code to reproduce figures in Lakshmikanth al - Immune system adaptation during Gender affirming Testosterone treatment.
For all the data in the article, please download data from https://zenodo.org/records/11517943 (DOI: 10.5281/zenodo.11517624). The data folder will have multiple folders, some that are Figure specific data and some that are more general for several figures (eg scRNA-seq data that we reuse over multiple figures).
To download all code, please clone this repository using git clone git@github.com:Brodinlab/Gender-affirming-Testosterone-treatment.git.
For jupyter scripts (python): For the file-pathways to work directly, open Jupyter Lab/Notebook in the specific figure-folder (eg figure-scripts/Figure2) and put the data-directory at the top of the folder (so the path is Gender-affirming-Testosterone-treatment/data), otherwise you can specify your own data directory.
For any questions regarding data analyses, please contact petter.brodin@ki.se