Bioconductor knowledge base - router

Task-oriented summaries of the official guide “Bioconductor Packages: Development, Maintenance, and Peer Review” (https://contributions.bioconductor.org). Open the file that matches the task. Each summary links back to its canonical chapter for the full text.

Start here

• New to submission, or want the whole path end to end: read workflow.md (the runbook).
• Just need one topic: use the map below.

Lifecycle router

Authoring a package:

• Naming: development/package-name.md (ch 2)
• General setup + key features: development/general-dev.md (ch 3-4)
• Reusing Bioc classes/methods (SummarizedExperiment, S4, etc.): development/methods-classes.md (ch 5)
• Metadata files (README, DESCRIPTION, NAMESPACE, NEWS, LICENSE, CITATION, INSTALL): development/metadata-files.md (ch 6-12)
• Documentation (vignettes, man pages, roxygen): development/documentation.md (ch 13)
• Package data + large data (ExperimentHub/AnnotationHub): development/data.md (ch 14)
• Unit tests: development/tests.md (ch 15)
• R code + Bioc code style: development/r-code.md (ch 16)
• Compiled / third-party code (C/C++/Fortran/Python): development/compiled-thirdparty.md (ch 17)
• Shiny apps: development/shiny.md (ch 18)
• AI policy + third-party code: development/ai-policy.md (ch 19)
• Non-software packages (ExperimentData/Annotation/Workflow): development/non-software-pkgs.md (ch 20)
• .gitignore: development/gitignore.md (ch 21)
• Build / Check / BiocCheck (the gate): development/build-check-bioccheck.md (ch 22-23)

Submitting:

• Eligibility, package types, tracker issue, Single Package Builder: 01-submissions.md (ch 1)
• The full sequence from local build to first release: workflow.md

Maintaining (after acceptance):

• Git workflow (BiocCredentials, git.bioconductor.org dual remotes), version numbering, build-report troubleshooting, deprecation, end of life, branch rename: maintenance.md (ch 24-30)

Reviewing (and what reviewers check):

• Review expectations, reviewer tools, volunteering: reviewer.md (ch 31-33)

Appendices:

• Using devel Bioconductor, advanced build options, querying web resources, C/Fortran, Mavericks, Rd links, NEWS, references: appendices.md (A-H)

The gate (memorize)

See workflow.md and development/build-check-bioccheck.md for detail, including which items are requirements and which are recommendations - the distinction matters when telling someone whether they can submit.

Requirements:

• Pass R CMD check clean on current R-devel (no errors, no warnings).
• Pass BiocCheck::BiocCheckGitClone() and BiocCheck::BiocCheck('new-package' = TRUE) clean.
• Individual files <= 5 MB.
• Include biocViews, a vignette, and man pages; valid maintainer email equal to the submitter; not already on CRAN; hosted on the GitHub default branch.

Recommendations (expected in practice, but upstream says should/recommended):

• Set Version: 0.99.0.
• Source build < 10 MB; R CMD check --no-build-vignettes < 10 min; < 8 GB memory to run vignettes/examples/tests.

Source: Bioconductor Packages: Development, Maintenance, and Peer Review Fetched 2026-08-14 from contributions.bioconductor.org (Bioconductor devel guide).