https://github.com/microbiome/miadash
Dashboard for microbiome data analysis with mia
https://github.com/microbiome/miadash
bioinformatics dashboard gui isee mia microbiome shiny visualisation webapp
Last synced: 2 months ago
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Dashboard for microbiome data analysis with mia
- Host: GitHub
- URL: https://github.com/microbiome/miadash
- Owner: microbiome
- Created: 2024-07-24T16:05:16.000Z (11 months ago)
- Default Branch: devel
- Last Pushed: 2025-03-27T10:06:31.000Z (3 months ago)
- Last Synced: 2025-04-10T05:14:55.101Z (2 months ago)
- Topics: bioinformatics, dashboard, gui, isee, mia, microbiome, shiny, visualisation, webapp
- Language: R
- Homepage: https://miadash-microbiome.2.rahtiapp.fi/
- Size: 1.44 MB
- Stars: 1
- Watchers: 1
- Forks: 4
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS
Awesome Lists containing this project
README
# miaDash 
[](https://github.com/microbiome/miaDash/issues)
[](https://github.com/microbiome/miaDash/pulls)
[](https://github.com/microbiome/miaDash/actions)
[](https://app.codecov.io/gh/microbiome/miaDash?branch=devel)
[](https://www.codefactor.io/repository/github/microbiome/miadash)
The goal of miaDash is to provide a user-friendly interface to import,
manipulate, analyse and visualise TreeSummarizedExperiment objects.
## Usage
miaDash is available online at [this address](https://miadash-microbiome.2.rahtiapp.fi/).
While suitable for small and medium datasets, the online version may slow down
when larger datasets are analysed (> 1000 features). In this case, the app can
be installed and run locally. Either way, functionality to subset and
agglomerate the data is also provided in the app.
## Installation instructions
The release version can be installed from Bioconductor as follows:
```
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("miaDash")
```
Contributors or users interested in the latest functionality can install the
devel version as follows:
```
remotes::install_github("microbiome/miaDash")
```
## Example
The basic functionality of miaDash can be explored as follows:
```
# Import miaDash
library(miaDash)
# Launch miaDash
if (interactive()) {
miaDash()
}
```
## Code of Conduct
Please note that the miaDash project is released with a
[Contributor Code of Conduct](https://bioconductor.org/about/code-of-conduct/).
By contributing to this project, you agree to abide by its terms. Contributions
are welcome in the form of feedback, issues and pull requests. You can find the
contributor guidelines of the miaverse
[here](https://github.com/microbiome/mia/blob/devel/CONTRIBUTING.md).
## Acknowledgements
miaDash results from the joint effort of the larger R/Bioconductor community. In
particular, this software mainly depends on the following packages:
- [_mia_](https://bioconductor.org/packages/release/bioc/html/mia.html)
- [_iSEEtree_](https://bioconductor.org/packages/devel/bioc/html/iSEEtree.html)
- [_iSEE_](https://www.bioconductor.org/packages/release/bioc/html/iSEE.html)
- [TreeSummarizedExperiment](https://www.bioconductor.org/packages/release/bioc/html/TreeSummarizedExperiment.html)
- [_shiny_](https://cran.r-project.org/web/packages/shiny/)