Analysis for Xenium figure in Bangs et al., 2026:
Tertiary lymphoid structures support the development of allergen-specific TCF1+ progenitor CD4+ T cells
This repo processes mouse lung 10x Xenium data (HDM/Flu) through two notebook pipelines, run in
numeric order. Each pipeline folder has its own README.md with a per-notebook table and the conda
environment used for each notebook (environment specs live in conda_envs/).
initial_processing/— builds the fully annotated AnnData object: assemble the scRNA-seq reference, predict cell-type labels with scANVI, refine them (including CITE-seq CD4 integration), define spatial zones with CellCharter, and identify TLS structures.downstream_analysis/— hypothesis testing and manuscript figures: squidpy neighborhood interactions, differential expression, distance-to-TLS / distance-to-bronchi and within-TLS radial analyses, and CellChat ligand–receptor analysis (05_cellchat/).
Other folders: inputs/ (small committed CSVs and color palettes), config/ (data/output paths),
utils/ (shared functions), geo/ (GEO submission prep), and hise_download/ (data download).
Analysis done by @kathleenabadie.