https://github.com/microbiome/microbiomedatasets

Experiment Hub based microbiome datasets
https://github.com/microbiome/microbiomedatasets

bioconductor experiment-hub microbiome microbiome-datasets

Last synced: 11 months ago
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Experiment Hub based microbiome datasets

• Host: GitHub
• URL: https://github.com/microbiome/microbiomedatasets
• Owner: microbiome
• Created: 2020-11-03T10:49:11.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2024-09-21T09:22:50.000Z (over 1 year ago)
• Last Synced: 2025-05-16T10:12:34.106Z (about 1 year ago)
• Topics: bioconductor, experiment-hub, microbiome, microbiome-datasets
• Language: R
• Homepage: https://bioconductor.org/packages/3.13/microbiomeDataSets/
• Size: 14.5 MB
• Stars: 6
• Watchers: 6
• Forks: 4
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS

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README

          
# `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.