{"id":20612683,"url":"https://github.com/datasnakes/rnaseek","last_synced_at":"2026-06-09T14:31:09.259Z","repository":{"id":216873399,"uuid":"94459370","full_name":"datasnakes/RNASeek","owner":"datasnakes","description":"A shiny app to perform single and multifactor differential analysis using DESeq2, edgeR, and limma","archived":false,"fork":false,"pushed_at":"2018-12-08T03:19:57.000Z","size":51020,"stargazers_count":2,"open_issues_count":4,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-06T18:27:23.083Z","etag":null,"topics":["count-table","deseq2","htseq","r","rna-seq","rnaseq","shiny","shiny-apps"],"latest_commit_sha":null,"homepage":"http://www.datasnakes.org/RNASeek","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/datasnakes.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}},"created_at":"2017-06-15T16:40:38.000Z","updated_at":"2024-01-12T18:36:52.000Z","dependencies_parsed_at":"2024-01-13T10:57:28.446Z","dependency_job_id":null,"html_url":"https://github.com/datasnakes/RNASeek","commit_stats":null,"previous_names":["datasnakes/rnaseek"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/datasnakes/RNASeek","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datasnakes%2FRNASeek","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datasnakes%2FRNASeek/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datasnakes%2FRNASeek/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datasnakes%2FRNASeek/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/datasnakes","download_url":"https://codeload.github.com/datasnakes/RNASeek/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datasnakes%2FRNASeek/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34112225,"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":"2026-06-09T02:00:06.510Z","response_time":63,"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":["count-table","deseq2","htseq","r","rna-seq","rnaseq","shiny","shiny-apps"],"created_at":"2024-11-16T11:07:38.488Z","updated_at":"2026-06-09T14:31:09.233Z","avatar_url":"https://github.com/datasnakes.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# RNASeek\n\nA shiny app to perform single and multifactor differential analyses using `edgeR`, `DESeq2`, or `limma` and create interactive visuzalizations. This app uses the output of a [`htseq-count-cluster`](https://github.com/datasnakes/htseq-count-cluster) merged counts table or merge counts table from [htseq](https://github.com/simon-anders/htseq)'s `htseq-count` script and a matching annotation table or csv file.\n\n\n## Running the RNASeek app locally\n\n### Via the runGitHub command\n\n```r\nlibrary(shiny)\nshiny::runGitHub('RNASeek', 'datasnakes')\n```\n\n### Via cloning the repository\n\n1. Clone or download the git repository.\n```bash\ngit clone https://github.com/datasnakes/RNASeek.git\n```\n\n2. Open RStudio or Rconsole and type:\n```r\nlibrary(shiny)\nrunApp('path/to/RNASeek')\n```\n## Dependencies\n\nThe dependencies are `shiny`, `shinythemes`, and  `DESeq2`. Ensure you have the latest versions installed and the latest version of R.\n\n\n### Update to the latest version of DESeq2\n\n```r\n## try http:// if https:// URLs are not supported\nsource(\"https://bioconductor.org/biocLite.R\")\nbiocLite(\"DESeq2\")\n```\n\n## Maintainers\n\nShaurita Hutchins | [@sdhutchins](https://github.com/sdhutchins) | [✉](mailto:sdhutchins@outlook.com)\n\nRob Gilmore | [@grabear](https://github.com/grabear) | [✉](mailto:robgilmore127@gmail.com)\n\nPlease feel free to [open an issue](https://github.com/datasnakes/RNASeek/issues/new) if you have a question, feedback, or problem using this app.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatasnakes%2Frnaseek","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatasnakes%2Frnaseek","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatasnakes%2Frnaseek/lists"}