{"id":22021631,"url":"https://github.com/lieberinstitute/recount3","last_synced_at":"2025-04-06T10:10:31.572Z","repository":{"id":41417567,"uuid":"255630219","full_name":"LieberInstitute/recount3","owner":"LieberInstitute","description":"Explore and download data from the recount3 project","archived":false,"fork":false,"pushed_at":"2024-12-10T22:03:21.000Z","size":3011,"stargazers_count":34,"open_issues_count":20,"forks_count":4,"subscribers_count":7,"default_branch":"devel","last_synced_at":"2025-03-30T09:08:29.955Z","etag":null,"topics":["annotation-agnostic","bioconductor","count","derfinder","exon","gene","human","illumina","junction","mouse","r","recount","recount3","rnaseq","rstats"],"latest_commit_sha":null,"homepage":"http://lieberinstitute.github.io/recount3","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/LieberInstitute.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}},"created_at":"2020-04-14T14:20:00.000Z","updated_at":"2025-03-25T17:07:59.000Z","dependencies_parsed_at":"2023-02-09T04:00:35.647Z","dependency_job_id":"585d953b-b75d-4381-ac80-b3fc754af950","html_url":"https://github.com/LieberInstitute/recount3","commit_stats":{"total_commits":250,"total_committers":7,"mean_commits":"35.714285714285715","dds":0.07199999999999995,"last_synced_commit":"da20bd4367b91f4196d716d81fa3700c59f95121"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Frecount3","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Frecount3/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Frecount3/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Frecount3/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LieberInstitute","download_url":"https://codeload.github.com/LieberInstitute/recount3/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247464220,"owners_count":20942970,"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","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":["annotation-agnostic","bioconductor","count","derfinder","exon","gene","human","illumina","junction","mouse","r","recount","recount3","rnaseq","rstats"],"created_at":"2024-11-30T06:13:24.379Z","updated_at":"2025-04-06T10:10:31.549Z","avatar_url":"https://github.com/LieberInstitute.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"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)\nlibrary(\"BiocStyle\")\n```\n\n# recount3 \u003cimg src=\"man/figures/logo.png\" align=\"right\" width=\"200px\" \u003e\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/recount3.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/recount3)\n[![Bioc devel status](http://www.bioconductor.org/shields/build/devel/bioc/recount3.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/recount3)\n[![Bioc downloads rank](https://bioconductor.org/shields/downloads/release/recount3.svg)](http://bioconductor.org/packages/stats/bioc/recount3/)\n[![Bioc support](https://bioconductor.org/shields/posts/recount3.svg)](https://support.bioconductor.org/tag/recount3)\n[![Bioc history](https://bioconductor.org/shields/years-in-bioc/recount3.svg)](https://bioconductor.org/packages/release/bioc/html/recount3.html#since)\n[![Bioc last commit](https://bioconductor.org/shields/lastcommit/devel/bioc/recount3.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/recount3/)\n[![Bioc dependencies](https://bioconductor.org/shields/dependencies/release/recount3.svg)](https://bioconductor.org/packages/release/bioc/html/recount3.html#since)\n[![Codecov test coverage](https://codecov.io/gh/LieberInstitute/recount3/branch/master/graph/badge.svg)](https://codecov.io/gh/LieberInstitute/recount3?branch=master)\n[![R build status](https://github.com/LieberInstitute/recount3/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/LieberInstitute/recount3/actions/workflows/check-bioc.yml)\n[![GitHub issues](https://img.shields.io/github/issues/LieberInstitute/recount3)](https://github.com/LieberInstitute/recount3/issues)\n[![GitHub pulls](https://img.shields.io/github/issues-pr/LieberInstitute/recount3)](https://github.com/LieberInstitute/recount3/pulls)\n\u003c!-- badges: end --\u003e\n\nThe `r Biocpkg('recount3')` R/Bioconductor package is part of the `recount3` project and is the latest iteration of the `ReCount` family of projects that provide access to uniformly-processed RNA sequencing datasets. The **main documentation website** for all the `recount3`-related projects is available at [**recount.bio**](https://LieberInstitute.github.io/recount3-docs). Please check that website for more information about how this R/Bioconductor package and other tools are related to each other.\n\n## Documentation\n\nFor more information about `r Biocpkg('recount3')` check the vignettes [through Bioconductor](http://bioconductor.org/packages/recount3) or at the [documentation website](http://lieberinstitute.github.io/recount3).\n\n## Installation instructions\n\nGet the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `r Biocpkg('recount3')` 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(\"recount3\")\n```\n\n## Citation\n\nBelow is the citation output from using `citation('recount3')` in R. Please \nrun this yourself to check for any updates on how to cite __recount3__.\n\n```{r 'citation', eval = requireNamespace('recount3')}\nprint(citation(\"recount3\"), bibtex = TRUE)\n```\n\nPlease note that `r Biocpkg('recount3')` 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 derfinderPlot project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). 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')`, `r BiocStyle::Githubpkg('r-hub/sysreqs')` 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://lieberinstitute.github.io/recount3) 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\n## Project history\n\nTo clarify the relationship between the R/Bioconductor packages and the phases of `ReCount` please check the table below:\n\n| Year | Phase | Main references | R/Bioconductor |\n| --- | --- | --- | --- |\n| 2011 | [`ReCount`](http://bowtie-bio.sourceforge.net/recount/) | DOI: [10.1186/1471-2105-12-449](https://doi.org/10.1186/1471-2105-12-449) | none |\n| 2017 | [`recount2`](https://jhubiostatistics.shinyapps.io/recount/) | DOI: [10.1038/nbt.3838](https://doi.org/10.1038/nbt.3838) [10.12688/f1000research.12223.1](https://doi.org/10.12688/f1000research.12223.1) | `r Biocpkg('recount')` |\n| 2021 | [`recount3`](https://LieberInstitute.github.io/recount3-docs) | DOI: [10.1186/s13059-021-02533-6](https://doi.org/10.1186/s13059-021-02533-6) | `r Biocpkg('recount3')` |\n\n## Teams involved\n\nThe `ReCount` family involves the following teams:\n\n* [Ben Langmead's lab at JHU Computer Science](http://www.langmead-lab.org/)\n* [Kasper Daniel Hansen's lab at JHBSPH Biostatistics Department](https://www.hansenlab.org/)\n* [Leonardo Collado-Torres](http://lcolladotor.github.io/) and [Andrew E. Jaffe](http://aejaffe.com/) from [LIBD](https://www.libd.org/)\n* [Abhinav Nellore's lab at OHSU](http://nellore.bio/)\n* [Jeff Leek's lab at JHBSPH Biostatistics Deparment](http://jtleek.com/)\n* Data hosted by the [Registry of Open Data on AWS](https://registry.opendata.aws/recount/) and [SciServer from IDIES at JHU](https://www.sciserver.org/) through a load balancer called [duffel](https://github.com/nellore/digitalocean-duffel).\n\n\n| | | | | |\n| --- | --- | --- | --- | --- |\n| \u003ca href=\"http://www.langmead-lab.org/\"\u003e\u003cimg src=\"http://www.langmead-lab.org/wp-content/uploads/2014/01/Screen-Shot-2014-02-02-at-5.20.13-PM-1024x199.png\" width=\"250px\"\u003e\u003c/a\u003e | \u003ca href=\"https://www.libd.org/\"\u003e\u003cimg src=\"http://lcolladotor.github.io/img/LIBD_logo.jpg\" width=\"250px\"\u003e\u003c/a\u003e | \u003ca href=\"http://nellore.bio/\"\u003e\u003cimg src=\"https://seekvectorlogo.net/wp-content/uploads/2018/08/oregon-health-science-university-ohsu-vector-logo.png\" width=\"250px\"\u003e\u003c/a\u003e | \u003ca href=\"https://www.sciserver.org/\"\u003e\u003cimg src=\"https://skyserver.sdss.org/dr14/en/images/sciserver_logo_inverted_vertical.png\" width=\"250px\"\u003e\u003c/a\u003e | \u003ca href=\"https://registry.opendata.aws/recount/\"\u003e\u003cimg src=\"https://assets.opendata.aws/img/AWS-Logo_White-Color_300x180.png\" width=\"250px\"\u003e\u003c/a\u003e |\n\n\n\u003cscript type='text/javascript' id='clustrmaps' src='//cdn.clustrmaps.com/map_v2.js?cl=ffffff\u0026w=300\u0026t=n\u0026d=4xd7F6p1BfdRypx-yEodrXiKhC0xvF0bJJywqR8rMKQ'\u003e\u003c/script\u003e\n\n\u003c!-- Global site tag (gtag.js) - Google Analytics --\u003e\n\u003cscript async src=\"https://www.googletagmanager.com/gtag/js?id=UA-163623894-1\"\u003e\u003c/script\u003e\n\u003cscript\u003e\n  window.dataLayer = window.dataLayer || [];\n  function gtag(){dataLayer.push(arguments);}\n  gtag('js', new Date());\n\n  gtag('config', 'UA-163623894-1');\n\u003c/script\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flieberinstitute%2Frecount3","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flieberinstitute%2Frecount3","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flieberinstitute%2Frecount3/lists"}