Analysis Code

This repository contains key analysis scripts and workflows used in our study on the cellular and molecular dynamics of human coronary atherosclerosis. Current Status Key analytical steps are included, such as: scCODA compositional analysis miloR neighborhood differential abundance testing Cellular composition dynamics across disease stages Cell-type heterogeneity and subclustering Trajectory inference (pseudotime analysis) Gene module identification Post-Publication Plan We will tag a stable release corresponding to the published version. A complete, end-to-end analysis pipeline will be made publicly available. The README will be updated with: Full citation information (DOI, journal, authors) Detailed usage instructions and workflow diagrams Reproducible software environment (e.g., R session info or renv/conda specifications) Note: This repository is shared to support transparency and scientific reproducibility. Scripts may be refactored for clarity and modularity after manuscript acceptance.