microeco

An R package for data mining in microbial community ecology

Background

In microbial community ecology, with the development of high-throughput sequencing techniques, the increasing data amount and complexity make the community data analysis and management a challenge. There has been a lot of R packages created for the microbiome profiling analysis. However, it is still difficult to perform data mining fast and efficiently. Therefore, we created R microeco package.

Main Features

• R6 Class to store and analyze data; fast, flexible and modularized
• Taxonomic abundance analysis
• Venn diagram
• Alpha diversity
• Beta diversity
• Differential abundance test
• Machine learning
• Null model analysis
• Network analysis
• Environmental data analysis
• Functional prediction

Install R/RStudio

If you do not already have R/RStudio installed, do as follows.

1. Install R
2. Install RStudio

Put R in the computer env PATH, for example your_directory\R-4.1.0\bin\x64

Open RStudio...Tools...Global Options...Packages, select the appropriate mirror in Primary CRAN repository.

Install microeco

Install microeco package from CRAN directly.

install.packages("microeco")

Or install the latest development version from github.

# If devtools package is not installed, first install it
install.packages("devtools")
# then install microeco
devtools::install_github("ChiLiubio/microeco")

Tutorial

See the detailed package tutorial (https://chiliubio.github.io/microeco_tutorial/). The backup tutorial website in gitee is also available (http://chiliubio.gitee.io/microeco_tutorial/). Please use the class name to search the help documents (e.g. ?microtable). Constructing the basic microtable object from other tools/platforms (e.g. QIIME, QIIME2, HUMAnN, Kraken2 and phyloseq) can be easily achieved with the package file2meco (https://github.com/ChiLiubio/file2meco).

Citation

Chi Liu, Yaoming Cui, Xiangzhen Li and Minjie Yao. 2021. microeco: an R package for data mining in microbial community ecology. FEMS Microbiology Ecology, 97(2): fiaa255. https://doi.org/10.1093/femsec/fiaa255

Contributing

We welcome any contribution, including but not limited to code, idea and tutorial. Please report errors and questions on github Issues. Any contribution via Pull requests or Email([email protected]) will be appreciated. By participating in this project you agree to abide by the terms outlined in the Contributor Code of Conduct.

References

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