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Ragomics-Meta: An open-source, scalable, reproducible, and extensible multi-omics analysis workflow
Zeping Gui1,2, Huidong Su3, Yuhao Chen2
1Department of Urology, Jiangsu Key Laboratory of Urological Disease Prevention and Treatment The Second Affiliated Hospital of Nanjing Medical University, Nanjing Medical University Nanjing China.
Abstract:
Ragomics-Meta is an open-source, scalable, and reproducible multi-omics workflow for metabolism-centered analysis (https://www.raganetwork.com/). It integrates scRNA/snRNA-seq, spatial transcriptomics, scATAC-seq, and metabolomics modules to support quality control, dimensionality reduction, clustering, differential expression and accessibility analyses, pathway activity scoring, cell-cell communication inference, transcription-factor network analysis, and spatial metabolism exploration. By incorporating established tools such as Scanpy, Seurat, Squidpy, COMMOT, SnapATAC2, MEBOCOST, scMetabolism, AUCell, and a curated gutMGene-based resource, Ragomics-Meta enables systematic characterization of tumor metabolic programs and host-microbiome interactions. AI-assisted interpretation further facilitates biological annotation and hypothesis generation, providing a user-friendly framework for integrative single-cell and spatial multi-omics analysis.
