{"id":15554883,"url":"https://github.com/ramiromagno/gwasrapidd","last_synced_at":"2025-04-13T06:42:33.949Z","repository":{"id":45945666,"uuid":"155549651","full_name":"ramiromagno/gwasrapidd","owner":"ramiromagno","description":"gwasrapidd: an R package to query, download and wrangle GWAS Catalog data","archived":false,"fork":false,"pushed_at":"2023-12-15T16:36:49.000Z","size":20864,"stargazers_count":95,"open_issues_count":5,"forks_count":14,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-24T11:54:23.041Z","etag":null,"topics":["association-studies","gwas-catalog","human","r","rest-client","snp","trait","trait-ontology"],"latest_commit_sha":null,"homepage":"https://rmagno.eu/gwasrapidd/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ramiromagno.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null}},"created_at":"2018-10-31T11:55:20.000Z","updated_at":"2024-12-19T09:20:37.000Z","dependencies_parsed_at":"2023-12-24T12:35:55.958Z","dependency_job_id":"be0f7ed0-b30e-4db8-a9eb-a4feef8a92ad","html_url":"https://github.com/ramiromagno/gwasrapidd","commit_stats":{"total_commits":376,"total_committers":5,"mean_commits":75.2,"dds":0.03191489361702127,"last_synced_commit":"88a4fca10e0127c5b28b5729903f36e10fd24d3f"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ramiromagno%2Fgwasrapidd","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ramiromagno%2Fgwasrapidd/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ramiromagno%2Fgwasrapidd/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ramiromagno%2Fgwasrapidd/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ramiromagno","download_url":"https://codeload.github.com/ramiromagno/gwasrapidd/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248675440,"owners_count":21143763,"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":["association-studies","gwas-catalog","human","r","rest-client","snp","trait","trait-ontology"],"created_at":"2024-10-02T15:04:03.783Z","updated_at":"2025-04-13T06:42:33.928Z","avatar_url":"https://github.com/ramiromagno.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 setup, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  # comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# gwasrapidd \u003cimg src=\"man/figures/logo.svg\" align=\"right\" height=140/\u003e\n\n[![CRAN status](https://www.r-pkg.org/badges/version/gwasrapidd)](https://CRAN.R-project.org/package=gwasrapidd)\n[![](https://img.shields.io/badge/doi-10.1093/bioinformatics/btz605-blue.svg)](https://doi.org/10.1093/bioinformatics/btz605)\n[![](https://img.shields.io/badge/Altmetric-38-yellow.svg)](https://www.altmetric.com/details/64505748)\n[![R build status](https://github.com/ramiromagno/gwasrapidd/workflows/R-CMD-check/badge.svg)](https://github.com/ramiromagno/gwasrapidd/actions)\n[![Codecov test coverage](https://codecov.io/gh/ramiromagno/gwasrapidd/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ramiromagno/gwasrapidd?branch=master)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)\n\nThe goal of `{gwasrapidd}` is to provide programmatic access to the [NHGRI-EBI\nCatalog](https://www.ebi.ac.uk/gwas) of published genome-wide association\nstudies.\n\nGet started by reading the\n[documentation](https://rmagno.eu/gwasrapidd/articles/gwasrapidd.html).\n\n## Installation\n\nInstall `{gwasrapidd}` from CRAN:\n\n``` r\ninstall.packages(\"gwasrapidd\")\n```\n\n## Cheatsheet\n\n\u003ca href=\"https://github.com/rstudio/cheatsheets/blob/master/gwasrapidd.pdf\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/rstudio/cheatsheets/master/pngs/gwasrapidd.png\" width=\"420\" height=\"300\"/\u003e\u003c/a\u003e\n\n## Example\n\nGet studies related to triple-negative breast cancer:\n\n```{r example1}\nlibrary(gwasrapidd)\nstudies \u003c- get_studies(efo_trait = 'triple-negative breast cancer')\nstudies@studies[1:4]\n```\n\nFind associated variants with study `r studies@studies$study_id[1]`:\n\n```{r example2}\nvariants \u003c- get_variants(study_id = 'GCST002305')\nvariants@variants[c('variant_id', 'functional_class')]\n```\n\n## Citing this work\n\n`{gwasrapidd}` was published in Bioinformatics in 2019:\nhttps://doi.org/10.1093/bioinformatics/btz605.\n\nTo generate a citation for this publication from within R:\n\n```{r citation}\ncitation('gwasrapidd')\n```\n\n## Code of Conduct\n  \nPlease note that the `{gwasrapidd}` project is released with a [Contributor Code\nof Conduct](https://rmagno.eu/gwasrapidd/CODE_OF_CONDUCT.html). By contributing\nto this project, you agree to abide by its terms.\n\n## Similar projects\n\n- Bioconductor R package *gwascat* by Vincent J Carey:\n[https://www.bioconductor.org/packages/release/bioc/html/gwascat.html](https://www.bioconductor.org/packages/release/bioc/html/gwascat.html)\n- Web application *PhenoScanner V2* by Mihir A. Kamat, James R. Staley, and\nothers:\n[http://www.phenoscanner.medschl.cam.ac.uk/](http://www.phenoscanner.medschl.cam.ac.uk/)\n- Web application *GWEHS: Genome-Wide Effect sizes and Heritability Screener* by\nEugenio López-Cortegano and Armando Caballero:\n[http://gwehs.uvigo.es/](http://gwehs.uvigo.es/)\n\n## Acknowledgements\n\nThis work would have not been possible without the precious help from the GWAS\nCatalog team, particularly [Daniel\nSuveges](https://www.ebi.ac.uk/about/people/daniel-suveges).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Framiromagno%2Fgwasrapidd","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Framiromagno%2Fgwasrapidd","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Framiromagno%2Fgwasrapidd/lists"}