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README.md
# mia - Microbiome analysis <img src="man/figures/mia_logo.png" align="right" width="120" /> <!-- badges: start --> [![R-CMD-check-bioc-devel](https://github.com/microbiome/mia/workflows/R-CMD-check-bioc-devel/badge.svg)](https://github.com/microbiome/mia/actions) <!--[![R-CMD-check-bioc](https://github.com/microbiome/mia/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/microbiome/mia/actions/workflows/check-bioc.yml)--> [![Codecov test coverage](https://codecov.io/gh/microbiome/mia/branch/master/graph/badge.svg)](https://codecov.io/gh/microbiome/mia?branch=master) <!-- badges: end --> ## 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.