wanjinhu / microeco

An R package for data analysis in microbial community ecology

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 microbiome 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 (abbreviated and pronounced as [miːkəu]).

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 tutorial can also be downloaded to the computer to open (https://github.com/ChiLiubio/microeco_tutorial/releases). Please use the class name to search the help documents (e.g., ?microtable). Creating 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 will be appreciated. By participating in this project you agree to abide by the terms outlined in the Contributor Code of Conduct.

References

• https://chiliubio.github.io/microeco_tutorial/references.html#references