Covers: Chapter 20 - Non-software packages

Non-Software Packages

Non-software packages fall into two families: annotation packages and experiment data packages. Hub-based distribution is preferred over self-contained data packages.

Annotation packages

  • Link identifiers (gene names, probe IDs) to related information (chromosomal location, Gene Ontology categories, mappings).
  • Must include proper documentation for the data provided.

Experiment data packages

  • Contain curated datasets from an experiment, course, or publication, typically a single dataset.
  • Require documentation of the data (source, creation, use).
  • Traditional self-contained experiment data packages are discouraged; prefer the Hub approach.

Hub packages (AnnotationHub / ExperimentHub)

  • Lightweight: data is stored externally (AWS S3, Azure Data Lakes, Ensembl, other public sites) and fetched on demand.
  • Must minimally contain: resource metadata, man pages describing the resources, and a vignette. May include supporting R functions.
  • Follow the CreateAHubPackage vignette in the HubPub package.

biocViews

  • Annotation packages must include AnnotationData (and appropriate child terms) in the DESCRIPTION biocViews: field.
  • Experiment data packages must include ExperimentData (and child terms).
  • Correct biocViews determine which of the three Bioconductor repositories the package is assigned to.

Submission

  • Submit through the GitHub package submission tracker.
  • Indicate the package type (annotation, experiment data, workflow) at submission.

Source: Non-software packages Fetched 2026-08-14 from contributions.bioconductor.org (Bioconductor devel guide).

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