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Primary DE model adjusted for sex covariate (~ condition + gender). Addresses the main biological weakness: unadjusted model despite having sex metadata. Results regenerated: 1,773 DE genes (was 1,902), 99.8% sign concordance with full cohort.
Workflow diagram added to README (ASCII pipeline visualization).
NA gender filtering added before balanced sampling and full-cohort analysis.
All figures, tables, and tests regenerated with the covariate-adjusted model. CI passes including full pipeline rebuild.