A multi-tissue immune map across 4,241 single-cell donors resolves asynchronous immune ageing

This repository contains analysis code, figure reports and reproducibility materials for the manuscript

A multi-tissue immune map across 4,241 single-cell donors resolves asynchronous immune ageing

Target journal: Nature Aging

The manuscript-facing package focuses on multi-tissue immune composition, gene-expression ageing trajectories, immune-age clocks and sex-associated differences in immune ageing.

Reproducibility package

Canonical Quarto reports and their supporting documentation live under vignettes/:

• Fig1_umap.qmd — multi-tissue immune-cell expression UMAPs
• Fig2.qmd — asynchronous ageing of immune-cell composition
• Fig4.qmd — immune-ageing trajectories and clocks
• Fig5.qmd — sex differences in immune ageing
• Fig*_supplementary_plots.qmd — supplementary analyses built from source-data workbooks
• plasma_niche_pseudobulk_qc.qmd — generates separate quality-controlled plasma, stromal and epithelial pseudobulks for the respiratory system and large intestine

For a lightweight reproduction using the shipped figure-ready objects:

export IMMUNE_HEALTHY_BODY_MAP_ROOT=/path/to/immuneHealthyBodyMap
export IMMUNE_HEALTHY_BODY_MAP_DATA=$IMMUNE_HEALTHY_BODY_MAP_ROOT/vignettes/data
Rscript vignettes/scripts/render_reports.R --mode reduced

See vignettes/README.md for the directory layout, configuration and full HPC recomputation workflow.

Plasma niche analysis inputs

The repository includes the complete input-generation workflow for plasma niche transcriptomics and pathway analyses. The parameterized interactive report retrieves healthy cellNexus single-cell data, applies dataset and sample QC, performs Seurat/Harmony integration and single-cell UMAP visualisation, aggregates pseudobulk counts and writes separate RDS objects for plasma, stromal and epithelial cells in the respiratory system and large intestine. The integrated Seurat object is also saved for reproducible visualisation.

quarto render vignettes/reports/plasma_niche_pseudobulk_qc.qmd

Generated data and QC summaries are written to the gitignored vignettes/data/processed/plasma_niche/ directory by default.

Data and fitted models

Large inputs are not stored in Git:

• Harmonised pseudobulk data: Zenodo 10.5281/zenodo.15798373
• Fitted sccomp L3 and L0 models: Zenodo 10.5281/zenodo.21389127
• Public cellNexus metadata 1.0.12: resolved by get_publication_metadata()
• Per-cell-type gene-model target stores: computational-data exemption requested; pipeline code is provided under vignettes/targets_pipeline/

The authoritative inventory and deposit decisions are documented in vignettes/manifests/.

Manuscript title

Use the following title verbatim in repository, archive and supplementary metadata:

A multi-tissue immune map across 4,240 single-cell donors resolves asynchronous immune ageing