https://github.com/microbiome/mia

Microbiome analysis
https://github.com/microbiome/mia

analysis bioconductor microbiome

Last synced: about 1 year ago
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Microbiome analysis

• Host: GitHub
• URL: https://github.com/microbiome/mia
• Owner: microbiome
• License: artistic-2.0
• Created: 2020-10-18T08:43:59.000Z (over 5 years ago)
• Default Branch: devel
• Last Pushed: 2025-05-15T20:18:58.000Z (about 1 year ago)
• Last Synced: 2025-05-15T20:31:04.139Z (about 1 year ago)
• Topics: analysis, bioconductor, microbiome
• Language: R
• Homepage: https://microbiome.github.io/mia/
• Size: 34.3 MB
• Stars: 51
• Watchers: 7
• Forks: 29
• Open Issues: 10
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

          
# mia - Microbiome analysis 

[![Platforms](http://bioconductor.org/shields/availability/release/mia.svg)](https://bioconductor.org/packages/release/bioc/html/mia.html)

[![rworkflows](https://github.com/microbiome/mia/actions/workflows/rworkflows.yml/badge.svg?branch=devel)](https://github.com/microbiome/mia/actions)

[![Bioc-release](http://bioconductor.org/shields/build/release/bioc/mia.svg)](http://bioconductor.org/packages/release/bioc/html/mia.html)

[![Bioc-age](http://bioconductor.org/shields/years-in-bioc/mia.svg)](https://bioconductor.org/packages/release/bioc/html/mia.html)

[![Codecov test

coverage](https://codecov.io/gh/microbiome/mia/branch/devel/graph/badge.svg)](https://codecov.io/gh/microbiome/mia?branch=devel)

[![Dependencies](http://bioconductor.org//shields/dependencies/release/mia.svg)](https://bioconductor.org/packages/release/bioc/html/mia.html)

## Using the package

This project provides functions and workflows examples for analyses

of microbiome data. The main class for working with microbiome data in this

package is `TreeSummarizedExperiment`. 

For examples of functionality, see the [function reference page](https://microbiome.github.io/mia/reference/index.html).

More information and example workflows are provided in the online

manual [Orchestrating Microbiome Analysis with

Bioconductor](https://microbiome.github.io/OMA).

## Installation

### Bioc-release

```

if (!requireNamespace("BiocManager", quietly = TRUE))

    install.packages("BiocManager")

BiocManager::install("mia")

```

### Bioc-devel

```

if (!requireNamespace("BiocManager", quietly = TRUE))

    install.packages("BiocManager")

# The following initializes usage of Bioc devel

BiocManager::install(version='devel')

BiocManager::install("mia")

```

## Contributing

Contributions are welcome in the form of feedback, issues, pull

requests etc, see [contributor guidelines](CONTRIBUTING.md).

## Code of conduct

Please note that the mia project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).

By contributing to this project, you agree to abide by its terms.