Scripts to reproduce results and plots

1. The "plot_meta_data.R" file is used to reproduce Figure 1a, Figure 1b, Figure 1c, Extended Data Figure 2a, Extended Data Figure 2b, Extended Data Figure 2c, Extended Data Figure 2d, Extended Data Figure 3d.

2. The "analysis_cell_composition_immune.R" file is used to reproduce Figure 1d, Figure 1e, Extended Data Figure 5a, Extended Data Figure 5b.

3. The "marker_gene_dotplot.R" file is used to reproduce Figure 1f, Figure 1i, Extended Data Figure 5d, Extended Data Figure 6e.

4. The "DEG_analysis_Tc17_vs_Th17.R" file is used to reproduce Extended Data Figure 5c.

5. The "DEG_analysis_Tc17_CD_vs_UC.R" file is used to reproduce Figure 1g and Figure 1h.

6. The "DEG_analysis_AREG+RTM_vs_APOE+RTM.R" file is used to reproduce Figure 1j and Figure 1k.

7. The "plot_rss_RTMs.R" file is used to reproduce Figure 1i and Figure 1m.

8. The "cell_type_enrichment.R" file is used to reproduce Figure 2a.

9. The "plot_heatmap.subset_specific_risk_genes.R" file is used to reproduce Figure 2c-d, Extended Data Figure 7a, and Extended Data Figure 8a.

10. The "cell_coposition_by_dataset.R" file is used to reproduce Extended Data Figure 2e.

11. The "examine_batch_correction.R" file is used to reproduce Extended Data Figure 3a-c

12. The "validate_celltype_by_dataset.R" file is used to reproduce Extended Data Figure 4a-c.

13. The "analyze_SCP259.R" file is used to reproduce Extended Data Figure 4d-g.

14. The "cell_composition_epi.R", "cell_composition_mes.R" and "cell_composition_endo.R" files were used to reproduce Extended Data Figure 6a-d.

15. The "compare_gex_by_group.R" file is used to reproduce Extended Data Figure 7b and Extended Data Figure 8b.

16. The "compare_regulons_between_disease_in_epithelial.R" is used to reproduce Extended Data Figure 10e,f.

17. The "major_cluster_color.txt" and "minor_cluster_color.txt" files provide color codes for major clusters and cell subtypes to reproduce these plots.

18. Code used to apply integration: scIBD_integration_code.