{"id":18189929,"url":"https://github.com/kullrich/vgwas","last_synced_at":"2026-01-21T02:09:06.927Z","repository":{"id":86806826,"uuid":"203729687","full_name":"kullrich/vGWAS","owner":"kullrich","description":"Variance Heterogeneity Genome-wide Association Study - Reimplementation","archived":false,"fork":false,"pushed_at":"2025-05-17T22:44:32.000Z","size":3424,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"devel","last_synced_at":"2025-05-17T23:24:37.072Z","etag":null,"topics":["gwas","vgwas"],"latest_commit_sha":null,"homepage":"https://kullrich.github.io/vGWAS/","language":"HTML","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/kullrich.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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":"2019-08-22T06:34:49.000Z","updated_at":"2025-05-17T22:44:26.000Z","dependencies_parsed_at":null,"dependency_job_id":"e32865a4-56bc-40a8-a351-93381d459dcf","html_url":"https://github.com/kullrich/vGWAS","commit_stats":{"total_commits":11,"total_committers":1,"mean_commits":11.0,"dds":0.0,"last_synced_commit":"62364ee95581f2d39dedf4534ae2515c5123fe06"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/kullrich/vGWAS","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2FvGWAS","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2FvGWAS/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2FvGWAS/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2FvGWAS/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kullrich","download_url":"https://codeload.github.com/kullrich/vGWAS/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2FvGWAS/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28622473,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-20T23:49:58.628Z","status":"online","status_checked_at":"2026-01-21T02:00:08.227Z","response_time":86,"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":["gwas","vgwas"],"created_at":"2024-11-03T04:04:34.286Z","updated_at":"2026-01-21T02:09:06.922Z","avatar_url":"https://github.com/kullrich.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# vGWAS\n[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg)](CODE_OF_CONDUCT.md)\n\nVariance Heterogeneity Genome-wide Association Study - Reimplementation\n=========\n\nR package source code: https://github.com/kullrich/vGWAS\n\nR package pages: https://kullrich.github.io/vGWAS/\n\nR package issues: https://github.com/kullrich/vGWAS/issues\n\nThis repository is a reimplementation from the original `vGWAS` R package from [Xia Shen](https://github.com/xiashen).\n\nsee the original publication\n[Inheritance Beyond Plain Heritability: Variance-Controlling Genes in Arabidopsis thaliana](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002839)\n\nsome function has been added to directly perform GWAS on genotype data obtained\nvia [plink](https://www.cog-genomics.org/plink/)\n\nthe function `vGWASparallel` has been added to perform statistical tests in parallel\nand work on genotype data encoded as sparse matrix\n\n## Installation\n\n### R specific installation prerequisites\n\n```\ninstall.packages(\"devtools\")\ninstall.packages(\"knitr\")\ninstall.packages(\"dglm\")\ninstall.packages(\"doParallel\")\ninstall.packages(\"foreach\")\ninstall.packages(\"genio\")\ninstall.packages(\"hglm\")\ninstall.packages(\"Matrix\")\ninstall.packages(\"onewaytests\")\n```\n\nInstall `vGWAS` package from [github](https://github.com/kullrich) using the [devtools](https://cran.r-project.org/web/packages/devtools/index.html) package.\n\n```\nlibrary(devtools)\ndevtools::install_github(\"kullrich/vGWAS\", build_vignettes = TRUE, dependencies = FALSE)\n```\n\n## Quick start\n\n```\nlibrary(vGWAS)\ndata(pheno)\ndata(geno.sparse)\ndata(chr)\ndata(map)\nvgwa \u003c- vGWASparallel(\n  phenotype = pheno,\n  geno.matrix = geno.sparse,\n  marker.map = map,\n  chr.index = chr,\n  geno.snp = \"row\"\n)\nplot(vgwa)\n```\n\n## Vignettes\n\nThese vignettes introduce `vGWAS`\n\n- [01. vGWAS basic tutorial](https://github.com/kullrich/vGWAS/blob/master/vignettes/vGWAS.Rmd)\n- [02. vGWAS plink tutorial](https://github.com/kullrich/vGWAS/blob/master/vignettes/vGWASsparse.Rmd)\n\n\n## Code of Conduct - Participation guidelines\n\nThis repository adhere to [Contributor Covenant](http://contributor-covenant.org) code of conduct for in any interactions you have within this project. (see [Code of Conduct](https://github.com/kullrich/CRBHits/-/blob/devel/CODE_OF_CONDUCT.md))\n\nSee also the policy against sexualized discrimination, harassment and violence for the Max Planck Society [Code-of-Conduct](https://www.mpg.de/11961177/code-of-conduct-en.pdf).\n\nBy contributing to this project, you agree to abide by its terms.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkullrich%2Fvgwas","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkullrich%2Fvgwas","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkullrich%2Fvgwas/lists"}