microeco 
An R package for data mining in microbial community ecology
Background
With the development of high-throughput sequencing techniques, the increasing data amount and complexity make the microbiome data analysis and management a challenge. Though there has been a lot of R packages created for the microbiome profiling analysis, it is still difficult to perform data mining fast, efficiently and comprehensively. Therefore, we created R microeco package (abbreviated and pronounced as [miΛkΙu]).
Main Features
- R6 Class to store and analyze data: 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.
Put R in the computer env PATH, for example your_directory\R-4.3.0\bin\x64
Open RStudio -> Tools -> Global Options -> Packages, select the appropriate mirror in Primary CRAN repository.
Install microeco
Install microeco package from CRAN.
install.packages("microeco")Or install the latest development version from github.
# If devtools package is not installed, first install it
install.packages("devtools")
devtools::install_github("ChiLiubio/microeco")Tutorial
Detailed online tutorial (https://chiliubio.github.io/microeco_tutorial/) is released along with the package.
The tutorial can also be downloaded to the computer to open (https://github.com/ChiLiubio/microeco_tutorial/releases).
When you are in an R session and want to have a look on those links, please run the command: ?microeco.
Please use a class name to search its help document (e.g., ?microtable) instead of the function therein.
Before creating a new issue in the Issues,
please read the guideline (https://chiliubio.github.io/microeco_tutorial/notes.html#github-issues).
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.