BioRAG-DE: benchmark data, prompts, model outputs, figures, and analysis code

This archive contains the benchmark materials, prompts, model outputs, scoring outputs, supplementary tables, manuscript figures, and analysis code for BioRAG-DE, a retrieval-assisted workflow for reconstructing executable differential-expression study designs from GEO task metadata. The package includes curated task definitions and gold-standard design references, locked model outputs, design-level scoring results, downstream concordance summaries, non-LLM and metadata-only control outputs, and scripts used to reproduce the reported analyses and figures. Raw public GEO expression data are not redistributed; accession identifiers and analysis scripts are provided for reproducibility.