Analysis scripts for: Robust within-participant inference for paired longitudinal mucosa-stool multi-omics (HMP2 ibdmdb cohort).

Paired mucosa-stool multi-omics: HMP2 IBD case study Analysis scripts for: Robust within-participant inference for paired longitudinal mucosa-stool multi-omics (HMP2 ibdmdb cohort). Layout a*.py - analysis & figure scripts (a15-a40 chain; lettered suffixes mark documented patches, see manuscript Methods) paper/results_S1|H2|H3/ - result tables (csv) paper/figures/ - final figures (png / eps / svg) How to run pip install numpy pandas scipy statsmodels matplotlib Scripts use relative paths (. = release root); run from here: python a15_hmp2_loader.py etc. Chain order: a15 loader/align -> a16-a18 H1 -> a20-a21 H2 -> a22-a24 H3 -> figures (a26c fig2, a27b fig3, a29c/a34c/a40b fig1/4) -> sensitivity (a31e, a35, a36). Environment Python 3.13.3; numpy / pandas / scipy / statsmodels / matplotlib (versions in manuscript Methods). Comments are partly in Chinese; all scientific claims are documented in the manuscript and its result tables.