Re-annotation of a fixed platelet-activation gene set to its stromal sources in gastric cancer: reproducible analysis code and result tables

It re-annotates a set of genes originally annotated by circulating-platelet-activation function (platelet-activation-annotated genes, PAG) to their actual cellular sources within gastric tumors, and quantifies how the resulting program relates to cancer-associated fibroblast (CAF) states and to the spatial distribution of CD8 T cells.The archive contains 37 R scripts organized into six ordered stages (bulk prognostic modeling, discovery single-cell cohort, spatial transcriptomics, independent single-cell replication, immunotherapy cohort, and reviewer robustness analyses); a frozen 11-gene LASSO-Cox coefficient table that is only loaded and never re-estimated downstream; four small input tables; 105 author-run result CSVs that serve as a table-by-table numerical reference; a dependency-check script; an English README with data access, directory layout, run order, random seeds and interpretive boundaries; and an MIT license.Analyses use public data: TCGA-STAD, GEO GSE84437/GSE15459/GSE183904/GSE150290/GSE251950, and ENA PRJEB25780.

Raw reads and large expression matrices are not included and must be obtained from these repositories following the README; the workflow reproduces all statistics and figures from the processed inputs. The global random seed is fixed at 2026 (42 for AUCell; 1000 CellChat permutations) and the reference environment is R 4.6.1. The archive supports result verification, method reuse, and follow-up work on stromal immune exclusion in gastric cancer.