<i>microeco</i>: an R package for data mining in microbial community ecology
2020/12/15 by Chi Liu, Yaoming Cui, Xiangzhen Li +1 · 37 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Gut microbiota and health #Microbial Community Ecology and Physiology #Genomics and Phylogenetic Studies
paper · doi:10.1093/femsec/fiaa255
openalex publication_date 2020/12/15 · openalex created_date 2020/12/21 · openalex updated_date 2026/07/28
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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