CXCR4-associated immune network and metabolite binding in tubulointerstitial injury of diabetic nephropathy

This repository contains the complete R Markdown codes and bioinformatic scripts used in our study on Diabetic Nephropathy (DN) using human renal tubular tissue data. The repository consists of the following sequential scripts: # Included Scripts: - 01_GSE99325_pipeline.R: Preprocessing, normalization, differential expression, and network preparation for the GSE99325 dataset.- 02_GSE30529_pipeline.R: Preprocessing, normalization, and expression analysis for the GSE30529 dataset.- 03_Integrative_DE_DKD.Rmd: Cross-cohort dataset integration, batch-effect correction, global differential expression analysis, and matrix structuring for network workflows.- 04_Co-expression_network_analysis.Rmd: WGCNA pipeline execution, including soft-thresholding power (beta) evaluation, gene module generation, and clinical module-trait correlation. Note on External Analyses:Downstream structural and network topology analyses including functional enrichment (clusterProfiler), PPI network extraction (STRING/Cytoscape), and molecular docking validation (AutoDock Vina for the CXCR4 receptor) were performed using specialized external software platforms as detailed in the methodology of the main manuscript. Note: Users should set their working directory to the repository root folder to ensure correct relative file paths during execution.