Processed data and reproducibility archive for phase-resolved transcriptomic bottlenecks in peptide cancer vaccine response

This dataset accompanies the manuscript “Phase-resolved transcriptomic bottlenecks in peptide cancer vaccine response.” The archive contains processed module-score tables, model-output tables, focused patient-level C2 expression values, prespecified gene-set definitions, supplementary methods audit files, and relative-path manuscript-level reproducibility scripts used to support the analyses reported in the manuscript. The original raw/source transcriptomic datasets remain available from the Gene Expression Omnibus under accession numbers GSE278476, GSE85698, and GSE53922. This Zenodo record provides the processed supporting data, tables, code, and audit materials needed for manuscript-level review and reproducibility. This is a secondary analysis of public data. The archive does not claim validated biomarker status, treatment-effect modification, causality, clinical decision utility, or product-release qualification; candidate panels are hypotheses for prospective validation.