PDF(Pubmed)
Abstract：
Over the last decades, the analysis of complex microbial communities by high-throughput sequencing of marker gene amplicons has become routine work for many research groups. However, the main challenges faced by scientists who want to make use of the generated sequencing datasets are the lack of expertise to select a suitable pipeline and the need for bioinformatics or programming skills to apply it. Here, we present MetaXplore, an interactive, user-friendly platform that enables the discovery and visualization of amplicon sequencing data. Currently, it provides a set of well-documented choices for downstream analysis, including alpha and beta diversity analysis, taxonomic composition, differential abundance analysis, identification of the core microbiome within a population, and biomarker analysis. These features are presented in a user-friendly format that facilitates easy customization and the generation of publication-quality graphics. MetaXplore is implemented entirely in the R language using the Shiny framework. It can be easily used locally on any system with R installed, including Windows, Mac OS, and most Linux distributions, or remotely via a web server without bioinformatic expertise. It can also be used as a framework for advanced users who can modify and expand the tool.
摘要：
在过去的几十年里，通过标记基因扩增子的高通量测序分析复杂的微生物群落已成为许多研究小组的常规工作。然而,想要利用生成的测序数据集的科学家面临的主要挑战是缺乏选择合适管道的专业知识，以及需要生物信息学或编程技能来应用它。这里,我们介绍MetaXplore，一个互动的，用户友好的平台，使扩增子测序数据的发现和可视化。目前,它为下游分析提供了一套有据可查的选择，包括α和β多样性分析，分类组成，差异丰度分析，识别群体中的核心微生物组，和生物标志物分析。这些功能以用户友好的格式呈现，便于轻松定制和生成出版物质量的图形。MetaXplore使用Shiny框架完全在R语言中实现。它可以在安装了R的任何系统上轻松地在本地使用，包括Windows,MacOS,和大多数Linux发行版，或通过没有生物信息学专业知识的网络服务器远程。它也可以用作高级用户的框架，这些用户可以修改和扩展该工具。
