This release contains: R scripts for Hedgehog pathway and ligand scoring, ratio-method scoring, Spearman correlation of Hedgehog scores with immune cell signatures, and figure generation. A modular RNA-seq workflow scaffold (scripts/00–06) covering renv bootstrapping, DESeq2 differential expression, Hallmark GSEA, volcano plots, and figure-traceability manifests for the companion MAPK15 16-sample cohort. figures (Hedgehog–immune correlation heatmap, ratio-method comparison plots, Hedgehog activation scatter panels) in results/figures/. Supporting result tables (Spearman ρ and FDR matrices, ratio-method scoring outputs, sample-level scores) in results/tables/. Code-to-figure traceability manifests in results/manifests/. Configuration template and sample metadata. Source data (TCGA TPM/RSEM matrix and raw featureCounts) are not redistributed; see data/*/README.md for retrieval instructions.