{"id":18077480,"url":"https://github.com/stephenturner/qqman","last_synced_at":"2025-04-13T02:15:45.088Z","repository":{"id":7797842,"uuid":"9168057","full_name":"stephenturner/qqman","owner":"stephenturner","description":"An R package for creating Q-Q and manhattan plots from GWAS results","archived":false,"fork":false,"pushed_at":"2024-03-18T16:56:08.000Z","size":18388,"stargazers_count":166,"open_issues_count":6,"forks_count":92,"subscribers_count":15,"default_branch":"master","last_synced_at":"2025-04-13T02:14:46.046Z","etag":null,"topics":["cran","genomics","gwas","r"],"latest_commit_sha":null,"homepage":"http://cran.r-project.org/web/packages/qqman/","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/stephenturner.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2013-04-02T10:45:40.000Z","updated_at":"2025-03-22T08:14:26.000Z","dependencies_parsed_at":"2022-08-21T05:50:10.084Z","dependency_job_id":"64a5a66a-3fbb-480b-a326-18f23f7242e2","html_url":"https://github.com/stephenturner/qqman","commit_stats":{"total_commits":95,"total_committers":7,"mean_commits":"13.571428571428571","dds":"0.18947368421052635","last_synced_commit":"f2ec247b6f31473f88a4b86e03a2349a4cfe3f1c"},"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stephenturner%2Fqqman","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stephenturner%2Fqqman/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stephenturner%2Fqqman/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stephenturner%2Fqqman/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/stephenturner","download_url":"https://codeload.github.com/stephenturner/qqman/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248654106,"owners_count":21140237,"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":["cran","genomics","gwas","r"],"created_at":"2024-10-31T11:44:25.755Z","updated_at":"2025-04-13T02:15:45.042Z","avatar_url":"https://github.com/stephenturner.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# qqman: An R package for creating Q-Q and manhattan plots from GWAS results.\n\n[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/qqman)](https://cran.r-project.org/package=qqman)\n\n[![DOI](https://joss.theoj.org/papers/10.21105/joss.00731/status.svg)](https://doi.org/10.21105/joss.00731)\n\n![qqman.gif](tools/qqman.gif)\n\n## Citation\n\nIf you'd like to cite qqman (appreciated but not required), please cite the publication below:\n\nTurner, (2018). qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. _Journal of Open Source Software_, 3(25), 731, https://doi.org/10.21105/joss.00731\n\nMore details are found in the preprint:\n\nTurner, S.D. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. [*biorXiv* DOI: 10.1101/005165](https://biorxiv.org/content/early/2014/05/14/005165).\n\n## Installation\n\nInstall the stable release from CRAN:\n\n```r\ninstall.packages(\"qqman\")\n```\n\nOr install directly from github using devtools\n\n```r\nlibrary(devtools)\ninstall_github(\"stephenturner/qqman\")\n```\n\nOr install the most recent development release with devtools (note, there be dragons here):\n\n```r\nlibrary(devtools)\ninstall_github(\"stephenturner/qqman\", ref=\"dev\")\n```\n\nLoad the package each time you use it:\n\n```r\nlibrary(qqman)\n```\n\n## Usage\n\nSee the [online package vignette](https://cran.r-project.org/package=qqman/vignettes/qqman.html) for more examples:\n\n```r\nbrowseVignettes(\"qqman\")\n```\n\nTake a look at the built-in data:\n\n```r\nhead(gwasResults)\n```\n\nBasic manhattan plot using built-in data:\n\n```r\nmanhattan(gwasResults)\n```\n\nBasic Q-Q plot using built-in data:\n\n```r\nqq(gwasResults$P)\n```\n\nGet help:\n\n```r\n?manhattan\n?qq\n```\n\n## Notes\n\n* This release is substantially simplified for the sake of maintainability and creating an R package. The old code that allows confidence intervals on the Q-Q plot and allows more flexible annotation and highlighting is still available at the [version 0.0.0 tag](https://github.com/stephenturner/qqman/tree/v0.0.0).\n* Special thanks to Dan Capurso and Tim Knutsen for useful contributions and bugfixes.\n* Thanks to all the blog commenters for pointing out bugs and other issues.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstephenturner%2Fqqman","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstephenturner%2Fqqman","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstephenturner%2Fqqman/lists"}