{"id":31617334,"url":"https://github.com/ropensci/gtexr","last_synced_at":"2026-03-04T12:31:46.634Z","repository":{"id":231189646,"uuid":"781175649","full_name":"ropensci/gtexr","owner":"ropensci","description":"An R interface to the GTEx Portal API","archived":false,"fork":false,"pushed_at":"2025-08-19T08:39:46.000Z","size":2198,"stargazers_count":12,"open_issues_count":3,"forks_count":3,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-01-12T03:25:11.506Z","etag":null,"topics":["api-wrapper","bioinformatics","eqtl","gtex","r","sqtl"],"latest_commit_sha":null,"homepage":"https://docs.ropensci.org/gtexr","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/ropensci.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":"codemeta.json","zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-04-02T22:11:06.000Z","updated_at":"2026-01-11T19:08:49.000Z","dependencies_parsed_at":"2024-09-18T15:36:52.416Z","dependency_job_id":"441c05de-9df8-4a0c-b1be-e90588964ccf","html_url":"https://github.com/ropensci/gtexr","commit_stats":null,"previous_names":["rmgpanw/gtexr","ropensci/gtexr"],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/ropensci/gtexr","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ropensci%2Fgtexr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ropensci%2Fgtexr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ropensci%2Fgtexr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ropensci%2Fgtexr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ropensci","download_url":"https://codeload.github.com/ropensci/gtexr/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ropensci%2Fgtexr/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30079737,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-04T12:28:08.313Z","status":"ssl_error","status_checked_at":"2026-03-04T12:27:28.210Z","response_time":59,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["api-wrapper","bioinformatics","eqtl","gtex","r","sqtl"],"created_at":"2025-10-06T12:57:35.762Z","updated_at":"2026-03-04T12:31:46.605Z","avatar_url":"https://github.com/ropensci.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)\n```\n\n# gtexr \u003ca href=\"https://docs.ropensci.org/gtexr/\"\u003e\u003cimg src=\"man/figures/logo.png\" align=\"right\" height=\"138\"/\u003e\u003c/a\u003e\n\n\u003c!-- badges: start --\u003e\n\n[![Codecov test coverage](https://codecov.io/gh/ropensci/gtexr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/ropensci/gtexr?branch=main) [![R-CMD-check](https://github.com/ropensci/gtexr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/gtexr/actions/workflows/R-CMD-check.yaml) [![Deploy to shinyapps.io](https://github.com/ropensci/gtexr/actions/workflows/shinyapps-deploy.yaml/badge.svg)](https://github.com/ropensci/gtexr/actions/workflows/shinyapps-deploy.yaml) [![CRAN status](https://www.r-pkg.org/badges/version/gtexr)](https://CRAN.R-project.org/package=gtexr) [![CRAN downloads](https://cranlogs.r-pkg.org/badges/gtexr)](https://CRAN.R-project.org/package=gtexr) [![CRAN downloads](https://cranlogs.r-pkg.org/badges/grand-total/gtexr)](https://CRAN.R-project.org/package=gtexr) [![Repo Status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/684_status.svg)](https://github.com/ropensci/software-review/issues/684) [![status](https://joss.theoj.org/papers/cacfc67c0fd0bd3ff269e68ef8ad795c/status.svg)](https://joss.theoj.org/papers/10.21105/joss.08249)\n\n\u003c!-- badges: end --\u003e\n\nThe goal of gtexr is to provide a convenient R interface to the [GTEx Portal API V2](https://gtexportal.org/api/v2/redoc#tag/GTEx-Portal-API-Info). \n\nThe [Genotype-Tissue Expression (GTEx) project](https://www.gtexportal.org/home/) is a comprehensive public resource for studying tissue-specific gene expression and regulation in human tissues. Through systematic analysis of RNA sequencing data from 54 non-diseased tissue sites across nearly 1000 individuals, GTEx provides crucial insights into the relationship between genetic variation and gene expression. This data is accessible through the [GTEx Portal API](https://gtexportal.org/api/v2/redoc#tag/GTEx-Portal-API-Info), enabling programmatic access to human gene expression data.\n\nNew to R but want to explore the available data? Try out the interactive no-code ⭐[shiny app](https://7hocgq-rmgpanw.shinyapps.io/gtexr/)⭐.\n\n## Installation\n\nYou can install this package from CRAN:\n\n``` r\ninstall.packages(\"gtexr\")\n```\n\nOr you can install the development version of gtexr from either [GitHub](https://github.com/ropensci/gtexr) with:\n\n``` r\n# install.packages(\"pak\")\npak::pak(\"ropensci/gtexr\") # source - GitHub\n```\n\n... or [R Universe](https://ropensci.r-universe.dev/builds) with:\n\n``` r\ninstall.packages(\"gtexr\", repos = \"https://ropensci.r-universe.dev\")\n```\n\n## Available functionality\n\n- **GTEx Portal API Info** – Retrieve general service information about the GTEx API.  \n- **Admin Endpoints** – Access maintenance messages and news updates from GTEx.  \n- **Static Association Endpoints** – Query precomputed eQTL and sQTL associations across tissues.  \n- **Dynamic Association Endpoints** – Perform on-the-fly eQTL and sQTL calculations.  \n- **Biobank Data Endpoints** – Retrieve metadata on biobank samples.\n- **Datasets Endpoints** – Access various GTEx dataset information, as well as variant annotation and linkage disequilibrium data.\n- **Expression Data Endpoints** – Obtain expression levels across tissues, including gene, exon, junction, and transcript-level data.  \n- **Histology Endpoints** – Retrieve tissue histology image data.  \n- **Reference Genome Endpoints** – Query reference genome features, including genetic coordinates for genes, transcripts and exons, as well as reported phenotype associations for a region.  \n\n## Examples\n\nGet general information about the GTEx service:\n\n```{r}\nlibrary(gtexr)\nget_service_info() |\u003e\n  tibble::glimpse()\n```\n\nRetrieve eQTL genes for whole blood tissue:[^1]\n\n[^1]: Note the warning raised if the number of items returned by a function call exceeds the requested page size. Argument `itemsPerPage` is set to 250 by default, but may be increased to ensure that all items are retrieved in one go.\n\n```{r get-eqtl-genes}\nget_eqtl_genes(\"Whole_Blood\")\n```\n\nRetrieve significant eQTLs for one or more genes:\n\n```{r get-significant-single-tissue-eqtls}\nget_significant_single_tissue_eqtls(gencodeId = c(\n  \"ENSG00000132693.12\",\n  \"ENSG00000203782.5\"\n))\n```\n\n## Citing gtexr\n\nIf you find gtexr useful, please consider citing both GTEx and gtexr. Citation details are available [here](https://docs.ropensci.org/gtexr/authors.html#citation).\n\nExample publications citing gtexr include:\n\n- [Schwartz R, Warwick AN, et al. Genetic Distinctions Between Reticular Pseudodrusen and Drusen: A Genome-Wide Association Study. Am J Ophthalmol. 2025 Mar 8:S0002-9394(25)00119-9. doi: 10.1016/j.ajo.2025.03.007. Epub ahead of print. PMID: 40064387](https://pubmed.ncbi.nlm.nih.gov/40064387/)\n\n## Community guidelines\n\nFeedback, bug reports, and feature requests are welcome; file issues or seek support [here](https://github.com/ropensci/gtexr/issues). If you would like to contribute to the package, please see our [contributing guidelines](https://docs.ropensci.org/gtexr/CONTRIBUTING.html).\n  \nPlease note that this package is released with a [Contributor Code of Conduct](https://ropensci.org/code-of-conduct/). By contributing to this project, you agree to abide by its terms.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fropensci%2Fgtexr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fropensci%2Fgtexr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fropensci%2Fgtexr/lists"}