MeTime is an opensource R package for reproducible analysis of longitudinal metabolomics data. It builds upon a central S4 container, metime_analyser, that stores multiple datasets, associated metadata and analysis outputs, enabling unified handling of complex longitudinal studies. Analyses are constructed by piping modular functions, beginning with data transformations (mod_), followed by calculations (calc_), and optional meta-analysis (meta_), so entire workflows remain transparent and easy to modify. MeTime wraps numerous existing methods within a consistent interface, including sample and metabolite distributions, correlation and distance matrices, dimensionality reduction (PCA, UMAP, tSNE), random forest imputation and feature selection via Boruta, eigenmetabolites and WGCNA based clustering, conservation index analysis, regression models (linear, mixed effects, and generalized additive), and partial correlation networks. By retaining all intermediate results and provenance within the container, MeTime facilitates iterative exploration and ensures reproducible reporting via automatically generated HTML and PDF outputs. Comprehensive user guides, case studies and reference documentation accompany the package, making MeTime a versatile platform for longitudinal omics workflows.

翻译：MeTime是一个用于可重复性分析纵向代谢组学数据的开源R包。它基于一个核心S4容器metime_analyser构建，该容器可存储多个数据集、关联元数据和分析输出，从而实现对复杂纵向研究的统一处理。分析通过管道式模块化函数构建，从数据转换（mod_模块）开始，依次执行计算（calc_模块）和可选的元分析（meta_模块），使整个工作流保持透明且易于修改。MeTime在统一接口中封装了多种现有方法，包括样本与代谢物分布、相关性与距离矩阵、降维（PCA、UMAP、tSNE）、基于Boruta算法的随机森林插补与特征选择、特征代谢物分析与WGCNA聚类、保守指数分析、回归模型（线性、混合效应和广义加性模型）以及偏相关网络。通过将所有中间结果和溯源信息保留在容器内，MeTime促进迭代探索，并通过自动生成的HTML和PDF输出确保可重复性报告。该软件包附有全面的用户指南、案例研究和参考文档，使其成为纵向组学工作流的通用平台。