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bioRxiv · 10.1101/2025.04.17.649266

EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research

Liu, B.·Liu, Y.·Xu, S.·Wu, Q.·Wu, D.·Zhan, L.·Liao, Y.·Mai, Y.·Zheng, M.·Wang, S.·Chen, Y.·Huang, Z.·Luo, X.·Xie, Z.·Pan, X.·Yu, G.·Xie, L.
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Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/649266v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@14dd0b1org.highwire.dtl.DTLVardef@1c04a79org.highwire.dtl.DTLVardef@159894dorg.highwire.dtl.DTLVardef@1454a01_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG HighlightsO_LIEasyMultiProfiler provides unified integration of microbial multi-omics data C_LIO_LIEasyMultiProfiler enables natural language-style analytical workflows C_LIO_LIEasyMultiProfiler solves key challenges in standardization and reproducibility C_LIO_LIEasyMultiProfiler extracts meaningful biological insights efficiently C_LI Host-microbiome interactions are crucial in maintaining physiological homeostasis and influencing disease progression. While traditional microbiome research, focused on microbial diversity and abundance, provided essential frameworks, the integration of multi-omics approaches established a far more comprehensive, systems-level understanding of microbiome functionality. However, significant methodological challenges in multi-omics data integration remain, including inconsistent sample coverage, heterogeneous data formats, and complex downstream analytical workflows. These challenges impact the reproducibility and reliability of results and underscore the critical requirement for developing standardized, systematic workflows. Thus, we developed the EasyMultiProfiler (EMP) workflow, a streamlined and efficient analytical framework for multi-omics data analysis. EMP provides a comprehensive infrastructure based on the SummarizedExperiment and MultiAssayExperiment classes, creating a unified framework for storing and analyzing omics data. The frameworks architecture comprises five interconnected functional modules: data extraction, preparation, support, analysis, and visualization. These modules are smoothly integrated into natural language-style analytical workflows, offering users an efficient and standardized solution for multi-omics analysis. EMP addresses critical challenges in multi-omics data analysis, including data integration, workflow standardization, and result reproducibility. The platforms modular architecture and intuitive interface provide researchers and clinicians with a robust, flexible workflow to systematically extract biologically relevant insights from complex multi-omics datasets.

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Liu, B., Liu, Y., Xu, S., Wu, Q., Wu, D., Zhan, L., Liao, Y., Mai, Y., Zheng, M., Wang, S., Chen, Y., Huang, Z., Luo, X., Xie, Z., Pan, X., Yu, G., Xie, L.. 2025-04-23. EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research. https://doi.org/10.1101/2025.04.17.649266

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