About

This book presents a comprehensive, R-based pipeline for metabolomics data analysis, from data preprocessing and normalization to network construction, visualization, and functional enrichment analysis. By integrating state-of-the-art tools such as WGCNA and MetaboAnalyst, the workflow enables systematic exploration of metabolomics datasets to uncover biologically meaningful patterns.

The pipeline has been applied in our published study: Ramzy, A., Abdelmoneim, T.K., Arafat, M., et al. (2025). Metabolomic analysis reveals key changes in amino acid metabolism in colorectal cancer patients. Amino Acids, 57, 22. https://doi.org/10.1007/s00726-025-03448-3

Acknowledgments
This pipeline builds upon the previous work of the bioinformaticians at the Proteomics Lab, 57357 Children’s Cancer Hospital Egypt (CCHE): Mohamed Soudy, Abdelrahman Atef, Ali Mostafa, Ahmed Karam, and Menna Arafat, as well as publicly available resources.

References
Horvath, S. (2011). Weighted network analysis: Applications in genomics and systems biology. Springer. https://doi.org/10.1007/978-1-4419-8819-5

Xia Lab. (2025, August 9). MetaboAnalystR Tutorial. MetaboAnalyst – MetaboAnalystR 4.0 Documentation. Retrieved August 24, 2025, from https://www.metaboanalyst.ca/docs/RTutorial.xhtml