{"id":14068286,"url":"https://github.com/lcolladotor/biocthis","last_synced_at":"2025-10-11T20:10:49.816Z","repository":{"id":40465841,"uuid":"259940445","full_name":"lcolladotor/biocthis","owner":"lcolladotor","description":"Automate package and project setup for Bioconductor packages","archived":false,"fork":false,"pushed_at":"2025-03-21T15:43:29.000Z","size":1221,"stargazers_count":54,"open_issues_count":14,"forks_count":17,"subscribers_count":6,"default_branch":"devel","last_synced_at":"2025-10-11T11:58:34.749Z","etag":null,"topics":["actions","bioconductor","biocthis","github","rstats","styler","usethis"],"latest_commit_sha":null,"homepage":"https://lcolladotor.github.io/biocthis/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lcolladotor.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":null,"code_of_conduct":".github/CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":".github/SUPPORT.md","governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2020-04-29T13:58:55.000Z","updated_at":"2025-10-06T09:31:18.000Z","dependencies_parsed_at":"2023-01-22T04:49:53.397Z","dependency_job_id":"a141fa8a-5985-41cd-b026-00f372166974","html_url":"https://github.com/lcolladotor/biocthis","commit_stats":{"total_commits":239,"total_committers":17,"mean_commits":"14.058823529411764","dds":"0.17991631799163177","last_synced_commit":"ba6e95e08d9226ba7472c05070b8234071c42399"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/lcolladotor/biocthis","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lcolladotor%2Fbiocthis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lcolladotor%2Fbiocthis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lcolladotor%2Fbiocthis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lcolladotor%2Fbiocthis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lcolladotor","download_url":"https://codeload.github.com/lcolladotor/biocthis/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lcolladotor%2Fbiocthis/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279008580,"owners_count":26084480,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-11T02:00:06.511Z","response_time":55,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["actions","bioconductor","biocthis","github","rstats","styler","usethis"],"created_at":"2024-08-13T07:06:04.526Z","updated_at":"2025-10-11T20:10:49.789Z","avatar_url":"https://github.com/lcolladotor.png","language":"R","readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n    collapse = TRUE,\n    comment = \"#\u003e\",\n    fig.path = \"man/figures/README-\",\n    out.width = \"100%\"\n)\n```\n\n# biocthis\n\n\u003c!-- badges: start --\u003e\n[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)\n[![Bioc release status](http://www.bioconductor.org/shields/build/release/bioc/biocthis.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/biocthis)\n[![Bioc devel status](http://www.bioconductor.org/shields/build/devel/bioc/biocthis.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/biocthis)\n[![Bioc downloads rank](https://bioconductor.org/shields/downloads/release/biocthis.svg)](http://bioconductor.org/packages/stats/bioc/biocthis/)\n[![Bioc support](https://bioconductor.org/shields/posts/biocthis.svg)](https://support.bioconductor.org/tag/biocthis)\n[![Bioc history](https://bioconductor.org/shields/years-in-bioc/biocthis.svg)](https://bioconductor.org/packages/release/bioc/html/biocthis.html#since)\n[![Bioc last commit](https://bioconductor.org/shields/lastcommit/devel/bioc/biocthis.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/biocthis/)\n[![Bioc dependencies](https://bioconductor.org/shields/dependencies/release/biocthis.svg)](https://bioconductor.org/packages/release/bioc/html/biocthis.html#since)\n[![Codecov test coverage](https://codecov.io/gh/lcolladotor/biocthis/branch/devel/graph/badge.svg)](https://codecov.io/gh/lcolladotor/biocthis?branch=devel)\n[![R build status](https://github.com/lcolladotor/biocthis/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/lcolladotor/biocthis/actions/workflows/check-bioc.yml)\n[![GitHub issues](https://img.shields.io/github/issues/lcolladotor/biocthis)](https://github.com/lcolladotor/biocthis/issues)\n[![GitHub pulls](https://img.shields.io/github/issues-pr/lcolladotor/biocthis)](https://github.com/lcolladotor/biocthis/pulls)\n\u003c!-- badges: end --\u003e\n\n`r BiocStyle::Githubpkg(\"lcolladotor/biocthis\")` is an R package that expands `r BiocStyle::CRANpkg(\"usethis\")` with Bioconductor-friendly templates. These templates will help you quickly create an R package that either has Bioconductor dependencies or that you are thinking of submitting to Bioconductor one day. `r BiocStyle::Githubpkg(\"lcolladotor/biocthis\")`  has functions that can also enhance your current R packages that either are already distributed by Bioconductor or have Bioconductor dependencies. `r BiocStyle::Githubpkg(\"lcolladotor/biocthis\")` also includes a Bioconductor-friendly [GitHub Actions](https://github.com/features/actions) workflow for your R package(s).\n\nNote that `r BiocStyle::Githubpkg(\"lcolladotor/biocthis\")` is not a Bioconductor-core package and as such it is not a Bioconductor official package. It was made by and for Leonardo Collado-Torres so he could more easily maintain and create Bioconductor packages as listed at [lcolladotor.github.io/pkgs/](https://lcolladotor.github.io/pkgs/). Hopefully `r BiocStyle::Githubpkg(\"lcolladotor/biocthis\")`  will be helpful for you too.\n\n## Installation instructions\n\nGet the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `biocthis` from [Bioconductor](http://bioconductor.org/) using the following code:\n\n```{r 'install', eval = FALSE}\nif (!requireNamespace(\"BiocManager\", quietly = TRUE)) {\n    install.packages(\"BiocManager\")\n}\n\nBiocManager::install(\"biocthis\")\n```\n\nAnd the development version from [GitHub](https://github.com/lcolladotor/biocthis) with:\n\n```{r 'install_dev', eval = FALSE}\nBiocManager::install(\"lcolladotor/biocthis\")\n```\n\n## Example\n\nHere is how you can use `r BiocStyle::Githubpkg(\"lcolladotor/biocthis\")` to create a new Bioconductor-friendly R package (illustrated using a temporary directory):\n\n```{r example, eval = requireNamespace('biocthis')}\n## Load biocthis\nlibrary(\"biocthis\")\n\n## Create an example package for illustrative purposes.\n## Note: you do not need to run this for your own package!\npkgdir \u003c- biocthis_example_pkg()\n\n## Create the bioc templates\nbiocthis::use_bioc_pkg_templates()\n```\n\nThe template `dev` scripts include comments and steps you can follow for making your Bioconductor-friendly R package or updating a current package. In particular, you might\nwant to use a Bioconductor-friendly GitHub Actions workflow. If this is your first time seeings this words, we highly recommend that you watch [Jim Hester's `rstudio::conf(2020)` talk on this subject](https://www.jimhester.com/talk/2020-rsc-github-actions/).\n\n```{r 'bioc_github_action', eval = FALSE}\n## Create a GitHub Actions workflow that is Bioconductor-friendly\nbiocthis::use_bioc_github_action()\n```\n\n```{r 'bioc_github_action_alternatives', eval = FALSE}\n## Alternatively, use the general GitHub Actions workflow maintained by\n## r-lib/actions\nusethis::use_github_action(\"check-standard\")\n```\n\n\n## Citation\n\nBelow is the citation output from using `citation('biocthis')` in R. Please\nrun this yourself to check for any updates on how to cite __biocthis__.\n\n```{r 'citation', eval = requireNamespace('biocthis')}\nprint(citation(\"biocthis\"), bibtex = TRUE)\n```\n\nPlease note that the `biocthis` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.\n\n## Code of Conduct\n\nPlease note that the `biocthis` project is released with a [Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By contributing to this project, you agree to abide by its terms.\n\n## Development tools\n\n* Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)  through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.\n* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.\n* The [documentation website](http://lcolladotor.github.io/biocthis) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.\n* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.\n* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.\n\nFor more details, check the `dev` directory.\n\nThis package was developed using `r BiocStyle::Biocpkg('biocthis')`.\n\n\n","funding_links":[],"categories":["R"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flcolladotor%2Fbiocthis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flcolladotor%2Fbiocthis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flcolladotor%2Fbiocthis/lists"}