Bioconductor/ai-agent-skills

bioc-pkg-dev

Guide an R package or a set of analysis scripts through Bioconductor submission: the pre-submission gate, the Contributions tracker, and post-acceptance maintenance

build-check-bioccheck

Run and interpret R CMD build, R CMD check, and both BiocCheck entry points against a Bioconductor package, separating real defects from environment gaps and known false positives

bioc-protocol-runner

Search, retrieve, evaluate trust, and execute citable workflows from federated protocol repositories

bioc-howto

A consolidated index of Bioconductor how-to skills covering genomics, sequencing, and omics data analysis tasks

adr-author

Write a new Architecture Decision Record following the established Nygard format and conventions.

check-bioconductor-skills

Verify that bioconductor/ai-agent-skills are available and help users find the right skill

document-skill

Automate documentation updates to SKILLS.md after creating or modifying a skill

create-skill

Help create a new AI agent skill through collaborative Q&A

bioc-pkg-finder

Find the R / Bioconductor packages best suited to a task or workflow

validate-skill

Validate that a skill conforms to the ai-agent-skills repository standards

create-package-instructions

Create complete AI instruction documentation for an R/Bioconductor package in .github/instructions/

analyze-r-package

Analyze R/Bioconductor package structure to extract key information about its purpose, exports, and characteristics

improve-code-coverage

Analyze R package code coverage using covr, classify testing gaps, and proactively write test cases to improve coverage and result correctness.

security-audit-r-package

Perform comprehensive security audit of R/Bioconductor packages

update-package-instructions

Update existing AI instruction documentation when an R/Bioconductor package changes

update-r-news

Draft or update an R package NEWS file from git commit history, examining diffs when commit messages are vague