{"id":25973470,"url":"https://github.com/jasdumas/shinygeo","last_synced_at":"2025-03-05T01:29:44.836Z","repository":{"id":31321588,"uuid":"34884069","full_name":"jasdumas/shinyGEO","owner":"jasdumas","description":"Gene Expression Omnibus Analysis with Shiny :microscope: ","archived":false,"fork":false,"pushed_at":"2022-06-02T00:37:44.000Z","size":376413,"stargazers_count":41,"open_issues_count":5,"forks_count":47,"subscribers_count":7,"default_branch":"master","last_synced_at":"2024-11-13T15:49:16.079Z","etag":null,"topics":["bioinformatics","data-visualization","gene-expression","r","shiny"],"latest_commit_sha":null,"homepage":"http://jasdumas.com/shinyGEO/","language":"CSS","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/jasdumas.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}},"created_at":"2015-05-01T00:52:11.000Z","updated_at":"2024-10-12T21:10:15.000Z","dependencies_parsed_at":"2022-09-06T01:11:05.598Z","dependency_job_id":null,"html_url":"https://github.com/jasdumas/shinyGEO","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jasdumas%2FshinyGEO","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jasdumas%2FshinyGEO/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jasdumas%2FshinyGEO/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jasdumas%2FshinyGEO/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jasdumas","download_url":"https://codeload.github.com/jasdumas/shinyGEO/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241948303,"owners_count":20047343,"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":["bioinformatics","data-visualization","gene-expression","r","shiny"],"created_at":"2025-03-05T01:29:44.229Z","updated_at":"2025-03-05T01:29:44.827Z","avatar_url":"https://github.com/jasdumas.png","language":"CSS","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Build Status](https://travis-ci.org/jasdumas/shinyGEO.svg?branch=master)](https://travis-ci.org/jasdumas/shinyGEO)\n\n[![Coverage Status](https://img.shields.io/codecov/c/github/jasdumas/shinyGEO/master.svg)](https://codecov.io/github/jasdumas/shinyGEO?branch=master)\n\n# shinyGEO\nshinyGEO is a web-based tool that allows a user to download the expression and sample data from a [Gene Expression Omnibus](http://www.ncbi.nlm.nih.gov/geo/browse/) dataset, select a gene of interest, and perform a survival or differential expression analysis using the available data. For both analyses, shinyGEO produces publication-ready graphics and generates R code ensuring that all analyses are reproducible. The tool is developed using shiny, a web application framework for R, a language for statistical computing and graphics.\n\n## Official Website\nhttp://gdancik.github.io/shinyGEO/\n\n## How to install this package?\n\nInstall the development version from Github:\n\n```r\nlibrary(devtools)\ninstall_github(\"jasdumas/shinyGEO\")\nlibrary(shinyGEO)\n```\n\n## How to use this package?\n\nUpdate the series and platform meta-data:\n\n```r\nshinyGEO::updateGEOdata()\n```\n\nLaunch the shiny application locally:\n\n```r\nshinyGEO::runshinyGEO()\n```\n\nOr launch the shiny application in a web browser:\n\n[http://bioinformatics.easternct.edu/shinyGEO/](http://bioinformatics.easternct.edu/shinyGEO/)\n\n## Contributors\n- Main contributors: Jasmine Daly, Michael Gargano, Garrett M. Dancik, PhD\n- Additional contributors: Ken-Heng Liao, Gregory Harper, Brandon Spratt\n\nPlease note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.\n\n## Acknowledgements\nThis work was supported, in part, by [Google Summer of Code funding to JD in 2015](https://www.google-melange.com/archive/gsoc/2015/orgs/rproject/projects/jasdumas.html). MG, KHL, GH, and BS contributed as part of an independent study in Computer Science / Bioinformatics while undergraduate students at Eastern Connecticut State University, Willimantic, CT,  USA.\n\n## Learn more\n- Read the abstract about `shinyGEO` published in [*Bioinformatics*](https://academic.oup.com/bioinformatics/article-abstract/32/23/3679/2525634/shinyGEO-a-web-based-application-for-analyzing).\n\n## Meta\n- Please [report any issues or bugs](https://github.com/jasdumas/shinyGEO/issues).\n- License: MIT\n- Get citation information for `shinyGEO` in R doing `r citation(package = 'shinyGEO')`\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjasdumas%2Fshinygeo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjasdumas%2Fshinygeo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjasdumas%2Fshinygeo/lists"}