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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# daa - Differential Abundance Analysis
<!-- badges: start -->
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](http://bioconductor.org/packages/release/bioc/html/daa.html)
[](https://app.codecov.io/gh/microbiome/daa)
<!-- badges: end -->
## Using the package
This package provides functions for differential abundance analysis (DAA)
of microbiome data. It works with `TreeSummarizedExperiment` and
`SummarizedExperiment` objects from the miaverse ecosystem.
**Available methods:**
- `getWilcoxon()` / `addWilcoxon()` - Wilcoxon rank-sum test
- `getTtest()` / `addTtest()` - t-test (Welch's or Student's)
For more information, see the [function reference](https://microbiome.github.io/daa/reference/index.html)
and the [Orchestrating Microbiome Analysis (OMA)](https://microbiome.github.io/OMA) online book.
## Installation
### Bioc-release
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("daa")
```
### Bioc-devel
```{r 'install_dev', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install(version = "devel")
BiocManager::install("daa")
```
## Contributing
Contributions are welcome in the form of feedback, issues, and pull requests.
See [contributor guidelines](CONTRIBUTING.md).
## Code of Conduct
Please note that the daa 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.