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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.

本仓库包含用于整合分析人类肝细胞癌（hepatocellular carcinoma, HCC）空间转录组学（spatial transcriptomics）、空间代谢组学（spatial metabolomics）与单细胞RNA测序（single-cell RNA sequencing）数据集的定制化分析脚本。该代码涵盖数据预处理、标准化、降维、聚类、空间映射、通路富集以及细胞-代谢物相互作用分析等核心分析环节。同时提供多组学层级整合分析流程，用于探究肝细胞癌微环境内肿瘤细胞的空间排布特征、免疫浸润状态与代谢异质性。所有脚本均采用R与Python语言编写，关键依赖项与运行参数均在对应文件中予以详细说明，以确保分析结果具备可复现性。