This R package is a collection of microbiome datasets published initially elsewhere. The data is available as TreeSummarizedExperiment or MultiAssayExperiment and a list of available dataset can be retrieved via the availableDataSets() function.

The aim is to provide datasets for teaching, example workflows or comparative efforts. If you have a dataset, which you like to see in this package, please let us know and/or provide a PR for the datasets.

Contribution

Feel free to contribute. Have a look at how existing datasets are organized and prepared data accordingly. It is also good to get in touch at the earliest convenience to discuss any issues.

Technical aspects

Let’s use a git flow kind of approach. Development version should be done against the master branch and then merged to master for the next release. (https://guides.github.com/introduction/flow/)

Resources on how data is added to Bioconductor’s ExperimentHub backend and accessed are available from Bioconductor here

Basic steps:

  • Assemble a TreeSummarizedExperiment from the raw data (Install the latest version from GitHub)
  • Save the individiual components as rds files in inst/extdata/hub// (If you have questions, have a look at the other datasets or check with us through online channels)
  • Prepare the metadata file, by creating a new metadata-.R in inst/scripts and run the script to create inst/extdata/metadata-.csv
  • Make sure that the metadata files passes the check by running AnnotationHubData::makeAnnotationHubMetadata(“../microbiomeDataSets”,“metadata-.csv”)

Code of conduct

Please note that the microbiomeDataSets project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.