Source data and analysis code for an evidence-gated HLA-II epitope prediction benchmark in autoimmune antigen presentation

This record contains the processed source data, benchmark input files, matched-control definitions, parsed prediction outputs, supplementary tables and analysis code supporting the manuscript “An evidence-gated benchmark for interpreting HLA-II epitope prediction signals in autoimmune antigen presentation”. The deposited files support an axis-dependent benchmark of HLA-II epitope prediction recovery across autoimmune disease-antigen-HLA contexts. The resource includes source data for figure generation, locked benchmark entities, matched background/control definitions, endpoint-aware prediction summaries, Monte Carlo analysis outputs, supplementary tables, code snapshots and additional scripts used for the v1.1 manuscript and figure updates. Third-party prediction tools and public databases used in the workflow are not redistributed when their licences do not permit redistribution. In those cases, the deposited code package provides wrapper scripts, input files, parsed outputs, version records and instructions for reproducing or auditing the analysis with the original third-party resources.