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This repository contains custom analysis scripts used for the integrated analysis of spatial transcriptomics, spatial metabolomics, and single-cell RNA sequencing datasets from human hepatocellular carcinoma (HCC). The code includes data preprocessing, normalization, dimensionality reduction, clustering, spatial mapping, pathway enrichment, and cell–metabolite interaction analysis. It also provides pipelines for integrating multi-omics layers to explore the spatial organization of tumor cells, immune infiltration, and metabolic heterogeneity within the HCC microenvironment. All scripts were written in R and Python, and key dependencies and parameters are documented in the corresponding files to ensure reproducibility.