ABSTRACT

A large amount of sequencing data is produced in microbial community ecology studies using the high-throughput sequencing technique, especially amplicon-sequencing-based community data. After conducting the initial bioinformatic analysis of amplicon sequencing data, performing the subsequent statistics and data mining based on the operational taxonomic unit and taxonomic assignment tables is still complicated and time-consuming. To address this problem, we present an integrated R package-‘microeco’ as an analysis pipeline for treating microbial community and environmental data. This package was developed based on the R6 class system and combines a series of commonly used and advanced approaches in microbial community ecology research. The package includes classes for data preprocessing, taxa abundance plotting, venn diagram, alpha diversity analysis, beta diversity analysis, differential abundance test and indicator taxon analysis, environmental data analysis, null model analysis, network analysis and functional analysis. Each class is designed to provide a set of approaches that can be easily accessible to users. Compared with other R packages in the microbial ecology field, the microeco package is fast, flexible and modularized to use and provides powerful and convenient tools for researchers. The microeco package can be installed from CRAN (The Comprehensive R Archive Network) or github (https://github.com/ChiLiubio/microeco).

中文翻译：

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microeco：用于微生物群落生态学数据挖掘的R包

摘要

使用高通量测序技术在微生物群落生态学研究中会产生大量测序数据，尤其是基于扩增子测序的群落数据。在对扩增子测序数据进行了初步的生物信息学分析之后，基于操作分类单元和分类分配表执行后续的统计和数据挖掘仍然是复杂且耗时的。为了解决这个问题，我们提出了一个集成的R包-'microeco'作为分析管道，用于处理微生物群落和环境数据。该软件包基于R6类系统开发，并结合了微生物群落生态研究中的一系列常用和高级方法。该软件包包括用于数据预处理，分类单元丰度图，维恩图，alpha多样性分析，beta多样性分析，差异丰度测试和指标分类法分析，环境数据分析，空模型分析，网络分析和功能分析。每个类旨在提供一组易于用户使用的方法。与微生物生态学领域中的其他R软件包相比，microeco软件包具有快速，灵活和模块化的使用方式，并为研究人员提供了强大而便捷的工具。可以从CRAN（综合R存档网络）或github（https://github.com/ChiLiubio/microeco）安装microeco软件包。每个类旨在提供一组易于用户使用的方法。与微生物生态学领域中的其他R软件包相比，microeco软件包具有快速，灵活和模块化的使用方式，并为研究人员提供了强大而便捷的工具。可以从CRAN（综合R存档网络）或github（https://github.com/ChiLiubio/microeco）安装microeco软件包。每个类旨在提供一组易于用户使用的方法。与微生物生态学领域的其他R软件包相比，microeco软件包具有快速，灵活和模块化的使用方式，并为研究人员提供了强大而便捷的工具。可以从CRAN（综合R存档网络）或github（https://github.com/ChiLiubio/microeco）安装microeco软件包。