microeco
An R package for data analysis in microbial community ecology
Science Score: 39.0%
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○CITATION.cff file
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✓.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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○Scientific vocabulary similarity
Low similarity (11.8%) to scientific vocabulary
Repository
An R package for data analysis in microbial community ecology
Basic Info
Statistics
- Stars: 243
- Watchers: 3
- Forks: 70
- Open Issues: 92
- Releases: 47
Metadata Files
README.md
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 omics data analysis and management a challenge. Though there has been a lot of R packages in this filed, it is still difficult to perform data mining fast, efficiently and comprehensively. Therefore, we created R microeco package (abbreviated and pronounced as [miːkəu]).
Main Features
- R6 Class to store and analyze data: flexible and modularized
- Data normalization
- 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, follow these steps:
Open RStudio -> Tools -> Global Options -> Packages, select the appropriate mirror in Primary CRAN repository.
Install microeco
Install microeco package from CRAN.
r
install.packages("microeco")
Or install the latest development version from Github.
```r
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/microecotutorial/) is released along with the package.
The tutorial can also be downloaded to the computer to open (https://github.com/ChiLiubio/microecotutorial/releases).
When the user is 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/microecotutorial/notes.html#github-issues).
Creating the basic microtable object from other tools/platforms (e.g. QIIME2, HUMAnN, Kraken2 and phyloseq)
can be easily achieved with the package file2meco (https://github.com/ChiLiubio/file2meco).
Additionally, to facilitate users' familiarity and utilization of the microeco package,
we have also developed a systematic protocol based on multi-omics data (https://github.com/ChiLiubio/microecoprotocol_v1).
Citation
Chi Liu, Felipe R. P. Mansoldo, Hankang Li, Alane Beatriz Vermelho, Raymond Jianxiong Zeng, Xiangzhen Li & Minjie Yao. A workflow for statistical analysis and visualization of microbiome omics data using the R microeco package. Nature Protocols (2025). https://doi.org/10.1038/s41596-025-01239-4
Chi Liu, Yaoming Cui, Xiangzhen Li and Minjie Yao. microeco: an R package for data mining in microbial community ecology. FEMS Microbiology Ecology, 2021, 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
Owner
- Name: Chi Liu
- Login: ChiLiubio
- Kind: user
- Location: Fujian Agriculture and Forestry University
- Repositories: 5
- Profile: https://github.com/ChiLiubio
R microbiology ecology
GitHub Events
Total
- Create event: 6
- Release event: 6
- Issues event: 115
- Watch event: 41
- Issue comment event: 197
- Push event: 95
- Fork event: 15
Last Year
- Create event: 6
- Release event: 6
- Issues event: 115
- Watch event: 41
- Issue comment event: 197
- Push event: 95
- Fork event: 15
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| ChiLiubio | l****6@1****m | 602 |
| Romain Francois | r****n@r****m | 2 |
| Felipe Mansoldo | m****f@g****m | 1 |
| Chen Tong | c****y@1****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 345
- Total pull requests: 0
- Average time to close issues: 5 months
- Average time to close pull requests: N/A
- Total issue authors: 171
- Total pull request authors: 0
- Average comments per issue: 3.21
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 84
- Pull requests: 0
- Average time to close issues: 17 days
- Average time to close pull requests: N/A
- Issue authors: 54
- Pull request authors: 0
- Average comments per issue: 2.04
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- apoosakkannu (28)
- marwa38 (17)
- jamorillo (17)
- DpennaS (12)
- alberjo296 (10)
- makerer5 (8)
- xinguo1236 (8)
- stefanom64 (8)
- milyzhou (6)
- jimena18-O (6)
- spencerlong1 (6)
- biazen123 (5)
- fpusan (5)
- guianrey (5)
- chrissy005 (4)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 3
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Total downloads:
- cran 2,983 last-month
- Total docker downloads: 9
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Total dependent packages: 3
(may contain duplicates) -
Total dependent repositories: 3
(may contain duplicates) - Total versions: 138
- Total maintainers: 1
proxy.golang.org: github.com/ChiLiubio/microeco
- Documentation: https://pkg.go.dev/github.com/ChiLiubio/microeco#section-documentation
- License: gpl-3.0
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Latest release: v1.15.0
published about 1 year ago
Rankings
proxy.golang.org: github.com/chiliubio/microeco
- Documentation: https://pkg.go.dev/github.com/chiliubio/microeco#section-documentation
- License: gpl-3.0
-
Latest release: v1.15.0
published about 1 year ago
Rankings
cran.r-project.org: microeco
Microbial Community Ecology Data Analysis
- Homepage: https://github.com/ChiLiubio/microeco
- Documentation: http://cran.r-project.org/web/packages/microeco/microeco.pdf
- License: GPL-3
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Latest release: 1.15.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.5.0 depends
- R6 * imports
- RColorBrewer * imports
- ape * imports
- data.table * imports
- dplyr * imports
- ggplot2 * imports
- grid * imports
- magrittr * imports
- reshape2 * imports
- rlang * imports
- scales * imports
- stats * imports
- tibble * imports
- vegan * imports
- GGally * suggests
- GUniFrac * suggests
- MASS * suggests
- agricolae * suggests
- ggdendro * suggests
- ggpubr * suggests
- ggrepel * suggests
- gridExtra * suggests
- igraph * suggests
- mice * suggests
- pheatmap * suggests
- picante * suggests
- randomForest * suggests
- rgexf * suggests