Appendix A β€” Contributing

OSTA is an open, community-driven resource that is designed to evolve alongside new methods, technologies, and best practices. Contributions are welcome from readers, users, and method developers, including feedback on clarity, suggestions for improvements, and extensions to existing content or workflows.

🌟 Why to contribute

There are several motivations for contributing:

  • Being publicly acknowledged within a trusted scientific ecosystem
  • Helping shape best practices in spatial (transcript)omics data analysis
  • Increasing the visibility and impact of your work through a widely used resource
  • Improving clarity and usability of a widely used educational resource
  • Ensuring new methods and technologies are represented in community standards
  • Supporting reproducible and transparent computational research practices

πŸ“Œ Ways to contribute

You can contribute in many ways:

  • Reporting typographical errors, issues,N or unclear sections
  • Improving explanations of methods or workflows
  • Adding new example analyses or methodological extensions
  • Extending platform or technology coverage
  • Improving reproducibility, performance, or overall clarity
  • Adding relevant literature, benchmarks, or external resources
    (e.g., in β€œFurther reading” or within chapter content)

βš™οΈ How to contribute

All contributions follow a GitHub-based workflow:

  1. Open an issue describing the problem or proposal
  2. Fork the repository and create a feature branch
  3. Implement changes in a reproducible manner
  4. Ensure the book renders successfully using Quarto
  5. Submit a pull request to the sandbox branch

πŸ” Review process

Contributions are evaluated for:

  • Scientific correctness and long-term maintainability
  • Consistency with OSTA structure and clarity of exposition
  • Computational reproducibility and successful build/check status

πŸ”¬ Reproducibility standards

All contributions must:

  • Run end-to-end without warnings or errors
  • Use Bioconductor-compatible dependencies
    (e.g., no Remotes: field in the DESCRIPTION)
  • Include session information (see existing chapters for formatting)
  • Be compatible with the target Bioconductor version, depending on the branch
  • Follow Bioconductor standards for package development (see guidelines)

βš–οΈ Community expectations

Contributors are expected to:

πŸ™ Accepted contributions will be recognized in the book’s Acknowledgments section.

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