{"id":16520804,"url":"https://github.com/jhrcook/tidy_gtex","last_synced_at":"2026-06-10T10:31:12.603Z","repository":{"id":115870898,"uuid":"185037361","full_name":"jhrcook/tidy_GTEx","owner":"jhrcook","description":"The GTEx data in a tidy format for use in R","archived":false,"fork":false,"pushed_at":"2019-05-05T17:03:24.000Z","size":6,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-03T01:15:46.364Z","etag":null,"topics":["gene-expression","gtex","r","tidy","tidyverse","tissue"],"latest_commit_sha":null,"homepage":"https://gtexportal.org/home/","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/jhrcook.png","metadata":{"files":{"readme":"README.Rmd","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":"2019-05-05T13:48:46.000Z","updated_at":"2019-05-05T17:04:54.000Z","dependencies_parsed_at":null,"dependency_job_id":"da4a968e-c362-4281-9871-993395387230","html_url":"https://github.com/jhrcook/tidy_GTEx","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/jhrcook/tidy_GTEx","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jhrcook%2Ftidy_GTEx","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jhrcook%2Ftidy_GTEx/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jhrcook%2Ftidy_GTEx/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jhrcook%2Ftidy_GTEx/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jhrcook","download_url":"https://codeload.github.com/jhrcook/tidy_GTEx/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jhrcook%2Ftidy_GTEx/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34149132,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-10T02:00:07.152Z","response_time":89,"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":["gene-expression","gtex","r","tidy","tidyverse","tissue"],"created_at":"2024-10-11T16:53:08.987Z","updated_at":"2026-06-10T10:31:12.578Z","avatar_url":"https://github.com/jhrcook.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\ntitle: \"Tidy GTEx\"\nauthor: \"Joshua Cook\"\ndate: \"2019-05-05\"\noutput: github_document\n---\n\n```{r setup, echo=FALSE, message=FALSE, warning=FALSE}\nknitr::opts_chunk$set(echo = TRUE, comments = \"#\u003e\")\n\nlibrary(jhcutils)\nlibrary(data.table)\nlibrary(magrittr)\nlibrary(tidyverse)\n```\n\n[![jhc github](https://img.shields.io/badge/GitHub-jhrcook-lightgrey.svg?style=flat\u0026logo=github)](https://github.com/jhrcook)\n[![jhc twitter](https://img.shields.io/badge/Twitter-JoshDoesaThing-00aced.svg?style=flat\u0026logo=twitter)](https://twitter.com/JoshDoesa)\n[![jhc website](https://img.shields.io/badge/Website-JoshDoesaThing-5087B2.svg?style=flat\u0026logo=telegram)](https://www.joshdoesathing.com)\n\n---\n\nThis repository hold the [Genotype-Tissue Expression (GTEx) project](https://gtexportal.org/home/) data in a tidy format for easy use with the R [tidyverse](https://www.tidyverse.org).\n\n\u003e \"The Genotype-Tissue Expression (GTEx) project is an ongoing effort to build a comprehensive public resource to study tissue-specific gene expression and regulation. Samples were collected from 53 non-diseased tissue sites across nearly 1000 individuals, primarily for molecular assays including WGS, WES, and RNA-Seq. Remaining samples are available from the GTEx Biobank. The GTEx Portal provides open access to data including gene expression, QTLs, and histology images.\"\n\n## Data\n\n**Latest download: May 5, 2019**\n\n\n\n\n\n---\n\n## Git Large File Storage\n\nThis repository uses git large file storage (\"git-lfs\") in order to manage the large data files.\n\n### Installation\n\nThe instructions on installing git-lfs for Mac, Windows, and some linux distros are available on the [git-lfs GitHub repo Wiki](https://github.com/git-lfs/git-lfs/wiki/Installation#source). Since I did this work remotely on the HMS Research Computing Cluster, I do not have root access and had to install from source. \n\n1. Download the source code of the latest release from [here](https://github.com/git-lfs/git-lfs/releases/latest).\n\n```bash\nwget https://github.com/git-lfs/git-lfs/releases/download/v2.7.2/git-lfs-v2.7.2.tar.gz\n```\n\n2. Build the binary using `go build -o /path/to/dest/git-lfs`, where `/path/to/dest/git-lfs` is the name of the directory you store your installed software in. This directory should be in your `$PATH`. For instance, I used `~/bin/git-lfs`.\n\n```bash\nmodule load go\ngo build -o ~/bin/git-lfs\n```\n\nThere should now be a file with the same path and name that you passed using the `-o` flag.\n\n3. Set up git-lfs in your git repository.\n\n```bash\ncd /path/to/my/git/repo\ngit lfs install\n#\u003e Updated git hooks.\n#\u003e Git LFS initialized.\n```\n\n4. Declare which files to track.\n\n```bash\ngit lfs track \"*.bigfiles\"\n#\u003e Tracking \"really_big_file.bigfiles\"\n#\u003e Tracking \"so_big_such_wow.bigfiles\"\n#\u003e Tracking \"large_files_rock.bigfiles\"\n```\n\nwhere `\"*.bigfiles\"` is the regular expression for large files in the repo.\n\n5. Track \".gitattributes\".\n\n```bash\ngit add .gitattributes\ngit commit .gitattributes -m \"start git-lfs\"\n```\n\nYou should now be able to add, commit, and push files like normal. Steps 1 and 2 only need to be done once per machine. Steps 3-5 need to be completed once per repository.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjhrcook%2Ftidy_gtex","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjhrcook%2Ftidy_gtex","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjhrcook%2Ftidy_gtex/lists"}