Introduction to ExperimentHubData (original) (raw)
Contents
- 1 Overview
- 2 Creating an ExperimentHub Package or Converting to an ExperimentHub Package
- 3 ExperimentHub_docker
Overview
ExperimentHubData provides tools to add or modify resources in Bioconductor’s ExperimentHub. This ‘hub’ houses curated data from courses, publications or experiments. The resources are generally not files of raw data (as can be the case in AnnotationHub) but instead are R / Bioconductorobjects such as GRanges, SummarizedExperiment, data.frame etc. Each resource has associated metadata that can be searched through the ExperimentHub client interface.
Creating an ExperimentHub Package or Converting to an ExperimentHub Package
Please see HubPub Vignette “CreateAHubPackage”.
vignette("CreateAHubPackage", package="HubPub")ExperimentHub_docker
The ExperimentHub_dockeroffers an isolated test environment for inserting / extracting metadata records in the ExperimentHub database. The README in the package explains how to set up the Docker and inserting records is done withExperimentHub::addResources().
In general this level of testing should not be necessary when submitting a package with new resources. The best way to validate record metadata is to read inst/extdata/metadata.csv with ExperimentHubData::makeExperimentHubMetadata(). If that is successful the metadata are ready to go.