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 microbiomeDataSets package focuses mainly on non-human studies. The independent curatedMetagenomicData package provides access to a large collection of standardized human microbiome studies in the same format.
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.
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.
Let’s use a gitflow 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 ExperimentHub documentation and in Creating ExperimentHub Package.
Basic steps:
Assemble a (Tree)SummarizedExperiment from the raw data
You can include the data creation script in inst/scripts/-data- (optional)
Save the individual data container components as rds files
Prepare the metadata file, by creating a new metadata-
Make sure that the metadata files passes the check by running a script like: ExperimentHubData::makeExperimentHubMetadata(“../microbiomeDataSets”,“3.13/metadata-hintikka-xo.csv”)
Maintainer will upload the data through their AWS login. The folder structure must match the one referenced in the metadata file; for example: microbiomeDataSets/<bioc.version.number>/lahti-ml/coldata.rds
Follow the instructions (See Section 7)
Afterwards, the maintainer will push the new metadata to Bioconductor git repo and inform hubs@bioconductor that there is new metadata. They will let us know when the upload is done.
In the meantime, prepare a loading function as found e.g. in microbiomeDataSets::LahtiMLData has to be created and push this to biocs git repo as well.
Bump the version (note that the version scheme is different)
For questions, have a look at the other datasets or check with us through online channels
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.