index.Rmd

--- 
title: "Bioconductor Packages: Development, Maintenance, and Peer Review"
author:
  - Kevin Rue-Albrecht
  - Daniela Cassol
  - Johannes Rainer
  - Lori Shepherd
  - Marcel Ramos Pérez
  - Martin Morgan
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
documentclass: book
bibliography: [book.bib, packages.bib]
biblio-style: apalike
link-citations: yes
description: "This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook."
---

# Welcome {-}

```{r, fig.align='center', echo=FALSE, out.height="200px"}
knitr::include_graphics("https://raw.githubusercontent.com/Bioconductor/BiocStickers/devel/Bioconductor/Bioconductor.png")
```

## Introduction {.unnumbered #intro}


The [_Bioconductor_][] project promotes high-quality, well documented, and interoperable software.
These guidelines help to achieve this objective; they are not meant to put undue
burden on package authors, and authors having difficultly satisfying guidelines
should seek advice on the [bioc-devel][bioc-devel-mail] mailing list.

Package maintainers are urged to follow these guidelines as closely as possible
when developing [_Bioconductor_][] packages.

General instructions for producing R packages can be found in the [Writing R
Extensions][] manual, available from within <i class="fab fa-r-project"></i>
(`RShowDoc("R-exts")`) or on the [R website][].

Remember these are the minimum requirements for package acceptance and the
package will still be subject to other guidelines below and a formal technical
review by trained [_Bioconductor_ package reviewer][reviewer-list] .


## Contribute {.unnumbered}

This book is open-source and hosted at <https://github.com/Bioconductor/pkgrevdocs>.
Contributions are welcome and encouraged in the form of forks and pull requests.

## Cite {.unnumbered}

Consider reading and citing our community guidelines article, "Eleven quick tips
for writing a Biconductor package" authored by @Soneson2025-zr. It provides a
concise overview for newcomers to [_Bioconductor_][] package development.

```{r include=FALSE}
# automatically create a bib database for R packages
knitr::write_bib(c(
  .packages(), 'bookdown', 'knitr', 'rmarkdown'
), 'packages.bib')
```

[_Bioconductor_]: https://bioconductor.org

[Abandon changes]: #abandon-changes
[add your public key to your GitHub account]: https://help.github.com/articles/connecting-to-github-with-ssh/
[Adding a new collaborator]: https://help.github.com/articles/inviting-collaborators-to-a-personal-repository/
[Adding a new SSH key to your GitHub account]: https://help.github.com/articles/adding-a-new-ssh-key-to-your-github-account/
[annotation-pkgs]: https://bioconductor.org/packages/release/data/annotation/
[annotation-views]: https://bioconductor.org/packages/release/BiocViews.html#___AnnotationData
[Azure Data Lakes]: https://azure.microsoft.com/en-us/services/data-lake-analytics
[Based on: Resolving a merge conflict]: https://www.atlassian.com/git/tutorials/using-branches/merge-conflicts
[bioc-common]: #reusebioc
[bioc-devel-mail]: https://stat.ethz.ch/mailman/listinfo/bioc-devel
[BiocParallel vignette]: https://bioconductor.org/packages/devel/bioc/vignettes/BiocParallel/inst/doc/Introduction_To_BiocParallel.pdf
[biocViews]: https://bioconductor.org/packages/devel/BiocViews.html
[BiocCredentials application]: https://git.bioconductor.org/BiocCredentials/
[build reports]: https://bioconductor.org/checkResults/
[build timings]: #propagate
[cirdep]: https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#submitting-related-packages
[Code Of Conduct]: https://bioconductor.github.io/bioc_coc_multilingual/
[Contributions]: https://github.com/Bioconductor/Contributions/issues/new
[CRAN foreign]: http://cran.r-project.org/doc/manuals/R-exts.html#System-and-foreign-language-interfaces
[CRAN config]: http://cran.fhcrc.org/doc/manuals/R-exts.html#Configure-and-cleanup
[CRAN's policy]: https://cran.r-project.org/web/packages/policies.html
[CRAN pkgs]: https://cran.r-project.org/web/packages/available_packages_by_name.html
[CRAN vigs]: http://cran.fhcrc.org/doc/manuals/R-exts.html#Writing-package-vignettes
[CRAN Rd]: http://cran.fhcrc.org/doc/manuals/R-exts.html#Rd-format
[Create A Hub Package]: https://bioconductor.org/packages/devel/bioc/vignettes/HubPub/inst/doc/CreateAHubPackage.html
[Create a local repository]: #create-local-repository
[Create a new GitHub repository]: #maintain-github-bioc
[Create a new GitHub account]: https://help.github.com/articles/signing-up-for-a-new-github-account/
[Create a new GitHub repo]: https://help.github.com/articles/create-a-repo/
[detect duplicate commits]: https://github.com/Bioconductor/bioc_git_transition/blob/master/misc/detect_duplicate_commits.py
[devel-LongTests-report]: https://bioconductor.org/checkResults/devel/bioc-longtests-LATEST/
[devel-GPU-report]: https://bioconductor.org/checkResults/devel/bioc-gpu-LATEST/
[devel-software-build-report]: https://bioconductor.org/checkResults/devel/bioc-LATEST/
['devel' version]: #use-devel
[docker]: https://bioconductor.org/help/docker/
[end-of-life policy]: #package-end-of-life-policy
[exptdata-pkgs]: https://bioconductor.org/packages/release/data/experiment/
[exptdata-views]: https://bioconductor.org/packages/release/BiocViews.html#___ExperimentData
[Fix bugs in devel and release]: #bug-fix-in-release-and-devel
[force-bioc-to-github]: #force-bioconductor-devel-to-github-devel
[Github collaborators]: https://docs.github.com/en/account-and-profile/setting-up-and-managing-your-github-user-account/managing-access-to-your-personal-repositories/inviting-collaborators-to-a-personal-repository
[git]: https://git.bioconductor.org
[git-repo-create]: https://help.github.com/articles/create-a-repo/
[gitver]: #git-version-control
[gitguides]: https://guides.github.com/
[git-and-github-learning-resources]: https://help.github.com/articles/git-and-github-learning-resources/
[git-scm]: https://git-scm.com/
[guidelines]: #develop-overview
[advanced-build-options]: #advanced-build-options
[Maintain a _Bioconductor_-only repository]: #maintain-bioc-only
[Maintain GitHub and _Bioconductor_ repositories]: #maintain-github-bioc
[Makevars files]: http://cran.r-project.org/doc/manuals/R-exts.html#Using-Makevars
[mergeconflict]: #resolve-merge-conflicts
[Merging a pull request]: https://help.github.com/articles/merging-a-pull-request/
[New package workflow]: #new-package-workflow
[Open github issue]: https://help.github.com/articles/creating-an-issue/
[Packages Under Review]: https://github.com/Bioconductor/Contributions/issues
[resolve duplicate commits]: #resolve-duplicate-commits
[Pull upstream changes]: #pull-upstream-changes
[Pull Requests]: https://help.github.com/articles/creating-a-pull-request/
[Push to GitHub and _Bioconductor_]: #push-to-github-bioc
[Rcpp Gallery]: http://gallery.rcpp.org/
[R CMD check environment]: #r-cmd-check-environment
[R Website]: http://cran.fhcrc.org/manuals.html
[R License]: https://www.r-project.org/Licenses/
[Registering native routines]: http://cran.fhcrc.org/doc/manuals/R-exts.html#Registering-native-routines
[release-schedule]: https://bioconductor.org/developers/release-schedule/
[release-biocviews]: http://bioconductor.org/packages/release/BiocViews.html
[release-LongTests-report]: https://bioconductor.org/checkResults/release/bioc-longtests-LATEST/
[release-GPU-report]: https://bioconductor.org/checkResults/release/bioc-gpu-LATEST/
[release-software-build-report]: https://bioconductor.org/checkResults/release/bioc-LATEST/
[Removing collaborator]: https://help.github.com/articles/removing-a-collaborator-from-a-personal-repository/
[Resolving a merge conflict using command line]: https://help.github.com/articles/resolving-a-merge-conflict-using-the-command-line/
[reviewer-list]: https://bioconductor.org/about/package-reviewers/
[reviewers zulip channel]: https://community-bioc.zulipchat.com/#narrow/channel/507978-reviewers
[rmarkdown]: http://rmarkdown.rstudio.com/
[rmarkdown documentation]: http://rmarkdown.rstudio.com/authoring_pandoc_markdown.html#citations
[shiny-posit]: https://shiny.posit.co/
[shiny-modules]: https://shiny.posit.co/r/articles/improve/modules/
[software-pkgs]: https://bioconductor.org/packages/release/bioc/
[support site]: https://support.bioconductor.org/
[support-register]: https://support.bioconductor.org/accounts/signup/
[Sync existing repositories]: #sync-existing-repositories
[testthat: Get Started with Testing]: http://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf
[Testing with testthat]: http://r-pkgs.had.co.nz/tests.html
[tracker]: https://github.com/Bioconductor/Contributions
[unit tests]: #tests
[versioning]:#versionnum
[which-remote-url-should-i-use]: https://help.github.com/articles/which-remote-url-should-i-use/
[wiki-license]: http://en.wikipedia.org/wiki/Comparison_of_free_software_licences
[Workflows]: #workflow-packages
[workflow-pkgs]: https://bioconductor.org/packages/release/workflows/
[Writing R Extensions]: https://cran.r-project.org/doc/manuals/R-exts.html
[workflow-views]: http://bioconductor.org/packages/devel/BiocViews.html#___Workflow

[BiocManager]: https://CRAN.R-project.org/package=BiocManager
[dotCall64]: https://CRAN.R-project.org/package=dotCall64
[formatR]: https://cran.r-project.org/web/packages/formatR/index.html
[microbenchmark]: https://cran.r-project.org/web/packages/microbenchmark
[Rcpp]: http://cran.r-project.org/web/packages/Rcpp/index.html
[reticulate]: https://rstudio.github.io/reticulate
[RUnit]: http://cran.r-project.org/web/packages/RUnit/index.html
[testthat]: http://cran.r-project.org/web/packages/testthat/index.html


[agile]: http://en.wikipedia.org/wiki/Agile_software_development
[bacon]: https://github.com/chneukirchen/bacon
[clang]: http://clang.llvm.org/
[cucumber]: https://cucumber.io
[gdb]: http://www.gnu.org/software/gdb/
[JUnit]: http://www.junit.org
[libc++]: http://libcxx.llvm.org/
[lldb]: http://lldb.llvm.org/
[PyUnit]: http://pyunit.sourceforge.net
[rspec]: https://rspec.info
[tdd]: http://en.wikipedia.org/wiki/Test-driven_development
[testy]: https://github.com/ahoward/testy
[Valgrind]: http://valgrind.org/
[Xcode]: https://developer.apple.com/xcode/