CD226-associated interferon and inflammatory programs in terminal-ileal γδ T and ILC3 cells in Crohn's disease — analysis code and processed data

Analysis code and processed data for a reanalysis of the public terminal-ileum single-cell RNA-sequencing atlas ArrayExpress E-MTAB-16986, characterising CD226 (DNAM-1) expression and CD226-associated transcriptional programs across terminal-ileal T and innate lymphoid cell populations in non-IBD controls and Crohn's disease. The analysis set comprises 181,164 T/ILC cells from 331 individuals (231 non-IBD controls, 100 Crohn's disease), analysed at the sample x annotation pseudobulk level. This record contains every script that turns the atlas into the reported numbers, the figure-layout scripts, all processed result tables underlying the manuscript's figures and supplementary tables, and the pseudobulk count matrices used for gene set enrichment analysis. The primary sequencing data are not redistributed here; they remain at E-MTAB-16986. The rendered figures are not redistributed either; the journal hosts them with the article, and the scripts that draw them are included.