# `microbiomeDataSets` This R package is a collection of microbiome datasets published initially elsewhere. The data is available as [`TreeSummarizedExperiment`](https://doi.org/doi:10.18129/B9.bioc.TreeSummarizedExperiment) or [`MultiAssayExperiment`](https://doi.org/doi:10.18129/B9.bioc.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](https://waldronlab.io/curatedMetagenomicData/index.html) 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. # 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 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](https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHub/inst/doc/ExperimentHub.html) and in [Creating ExperimentHub Package](https://bioconductor.org/packages/release/bioc/vignettes/AnnotationHub/inst/doc/CreateAHubPackage.html). 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-.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 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//lahti-ml/coldata.rds - Follow the [instructions](https://bioconductor.org/packages/release/bioc/vignettes/AnnotationHub/inst/doc/CreateAHubPackage.html) (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](microbiome.github.io) # Code of conduct Please note that the microbiomeDataSets 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.

近期下载者：

相关文件：

评论：[我要评论] [举报此文件]

收藏者：