Analysis code and intermediate result tables for: A THBS1-CCL2/CCR1-macrophage axis links metabolic syndrome to kidney stones

This record contains the analysis code and intermediate result tables supporting the manuscript "A THBS1-CCL2/CCR1-macrophage axis links metabolic syndrome to kidney stones: an integrated transcriptomic and immune infiltration analysis" (Tao & Xu, 2026). The archive reproduces the complete analysis pipeline: (1) differential expression analysis of peripheral blood mononuclear cell (PBMC) transcriptomes from a metabolic syndrome (MetS) cohort (GSE98895) and a kidney stone disease cohort (GSE318167) with limma and DESeq2, and intersection of the genes changed in the same direction; (2) construction of the co-expression network of the 18 shared genes, partitioning into four modules and visualisation in Cytoscape; (3) GO and KEGG enrichment of each module and xCell2 deconvolution of immune cell enrichment scores; (4) module-immune and gene-immune correlation analysis; (5) composition-adjusted sensitivity analyses and mediation analysis of the THBS1-CCR1/CCL2-macrophage axis; and (6) replication of the core analyses in the independent MetS cohort GSE200744. All input data are publicly available from the Gene Expression Omnibus under the accessions above; no new human samples were generated in this study. Analyses were performed in R 4.6.0 and Python 3.13. Contents: code/ (analysis scripts and figure assembly scripts), results/ (Supplementary Tables S1-S4 and intermediate statistics), README.md (software requirements, execution order, expected outputs).