Contributing to curatedMetagenomicData
curatedMetagenomicData aims to embody the spirit of open-source software, reproducibility, and to provide an ever growing collection of metagenomic data. As such, reports of bugs and curation errors, and suggestions and curation of relevant new metagenomic datasets will gladly be accepted.
The package is described at https://waldronlab.github.io/curatedMetagenomicData/, including information for installation and example analyses.
Reporting Bugs and Errors in Curation
If you are able to fix a bug yourself, or wish to add an analysis example, we would welcome a pull request. If the pull request builds cleanly on the continuous itegration servers it will be merged as soon as is possible.
Addition of Datasets to curatedMetagenomicData
Authors welcome the addition of new metagenomic datasets provided that the raw data are hosted by NCBI/SRA and can be run through our MetaPhlAn2 and HUMAnN2 pipeline. You can request the addition of a dataset by opening an issue on the issue tracker, pointing us to the publication and raw data.
You can speed up our ability to incorporate a new dataset by providing curated metadata. See https://github.com/waldronlab/curatedMetagenomicDataCuration for instructions on how to curate a new dataset.
Using the curatedMetagenomicData Pipeline Yourself
If you have an issue that is not documented elsewhere, visit the Bioconductor support site at https://support.bioconductor.org/, briefly describe your issue, and add the tag curatedMetagenomicData.