Computationnal code for analysis of patients' PBMC with Aicardi-Goutières syndrome

Annotated code to reproduce all computationnal analyses from the paper entitled "Pharmacological stabilization of hypoxia-inducible factor 1-alpha dampens the interferon response while favoring glycolysis pathway in Aicardi-Goutières syndrome" Batignes et al. accepted in Nature Communications in january 2026. A "Ressources" files is recquire to run the code and available on Figshare under DOI:10.6084/m9.figshare.31055725 . It contains processed CITE-seq/scRNA-seq data, metabolomic data and gene lists. Raw scRNA-seq data are available on GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE220764 Most of the code is in R (.R file) but gene regulatory network figures have been generated on python (jupiter .ipynb file).