The rapid evolution of mass spectrometry (MS)-based lipidomics has enabled the simultaneous measurement of numerous lipid classes. With lipidomics datasets becoming increasingly available, lipidomic-focused software tools are required to facilitate data analysis as well as mining of public datasets, integrating lipidomics-unique molecular information such as lipid class, chain length, and unsaturation. To address this need, we developed lipidr, an open-source R/Bioconductor package for data mining and analysis of lipidomics datasets. lipidr implements a comprehensive lipidomic-focused analysis workflow for targeted and untargeted lipidomics. lipidr imports numerical matrices, Skyline exports, and Metabolomics Workbench files directly into R, automatically inferring lipid class and chain information from lipid names. Through integration with the Metabolomics Workbench API, users can search, download, and reanalyze public lipidomics datasets seamlessly. lipidr allows thorough data inspection, normalization, and uni- and multivariate analyses, displaying results as interactive visualizations. To enable interpretation of lipid class, chain length, and total unsaturation data, we also developed and implemented a novel lipid set enrichment analysis. A companion online guide with two live example datasets is presented at https://www.lipidr.org/. We expect that the ease of use and innovative features of lipidr will allow the lipidomics research community to gain novel detailed insights from lipidomics data.

中文翻译：

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脂质体：用于脂质组学数据集的数据挖掘和分析的软件工具。

基于质谱（MS）的脂质组学的快速发展使得能够同时测量多种脂质类别。随着脂质组学数据集的日益可用，需要以脂质组学为重点的软件工具来促进数据分析和公共数据集的挖掘，整合脂质组学独特的分子信息，例如脂质类别，链长和不饱和度。为了满足这一需求，我们开发了lipoter，这是一种开源R / Bioconductor软件包，用于数据挖掘和脂质组学数据集的分析。他针对目标和非目标脂质组学实施了全面的针对脂质组学的分析工作流程。脂质剂将数字矩阵，Skyline导出和代谢组学工作台文件直接导入R，从脂质名称自动推断脂质类别和链信息。通过与Metabolomics Workbench API集成，用户可以无缝搜索，下载和重新分析公共脂质组学数据集。它可以进行彻底的数据检查，规范化以及单变量和多变量分析，并以交互式可视化方式显示结果。为了能够解释脂质类别，链长和总不饱和度数据，我们还开发并实施了新型脂质集富集分析。https://www.lipidr.org/上提供了带有两个实时示例数据集的配套在线指南。我们期望脂质剂的易用性和创新功能 将使脂质组学研究社区从脂质组学数据中获得新颖的详细见解。