生物
R包
管道(软件)
生态学
扩增子测序
微生物生态学
数据挖掘
群落结构
微生物种群生物学
预处理器
领域(数学)
计算机科学
数据科学
人工智能
纯数学
遗传学
计算科学
16S核糖体RNA
细菌
数学
程序设计语言
作者
Chi Liu,Yaoming Cui,Xiangzhen Li,Minjie Yao
标识
DOI:10.1093/femsec/fiaa255
摘要
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).
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