{"id":14068255,"url":"https://github.com/JoachimGoedhart/VolcaNoseR","last_synced_at":"2025-07-30T03:32:39.964Z","repository":{"id":55992035,"uuid":"233691130","full_name":"JoachimGoedhart/VolcaNoseR","owner":"JoachimGoedhart","description":"Shiny app for making and annotating Volcano plots","archived":false,"fork":false,"pushed_at":"2024-08-21T13:10:17.000Z","size":497,"stargazers_count":21,"open_issues_count":3,"forks_count":7,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-12-04T09:39:05.041Z","etag":null,"topics":["dataviz","genomic-data-analysis","ggplot2","proteomics-data-analysis","shiny","shinyapp","volcano"],"latest_commit_sha":null,"homepage":"https://huygens.science.uva.nl/VolcaNoseR/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/JoachimGoedhart.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":"2020-01-13T20:52:04.000Z","updated_at":"2024-10-16T01:22:06.000Z","dependencies_parsed_at":"2023-01-23T14:00:14.340Z","dependency_job_id":null,"html_url":"https://github.com/JoachimGoedhart/VolcaNoseR","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/JoachimGoedhart/VolcaNoseR","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JoachimGoedhart%2FVolcaNoseR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JoachimGoedhart%2FVolcaNoseR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JoachimGoedhart%2FVolcaNoseR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JoachimGoedhart%2FVolcaNoseR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JoachimGoedhart","download_url":"https://codeload.github.com/JoachimGoedhart/VolcaNoseR/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JoachimGoedhart%2FVolcaNoseR/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267803984,"owners_count":24146527,"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","status":"online","status_checked_at":"2025-07-30T02:00:09.044Z","response_time":70,"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":["dataviz","genomic-data-analysis","ggplot2","proteomics-data-analysis","shiny","shinyapp","volcano"],"created_at":"2024-08-13T07:06:03.207Z","updated_at":"2025-07-30T03:32:39.535Z","avatar_url":"https://github.com/JoachimGoedhart.png","language":"R","funding_links":[],"categories":["R"],"sub_categories":[],"readme":"# VolcaNoseR\nA Shiny App for making Volcano plots\n\n\n### Running the App\n\nThe web-tool runs from a shiny server, and can be accessed at:\n\no [https://huygens.science.uva.nl/VolcaNoseR/](https://huygens.science.uva.nl/VolcaNoseR/)\n\no [https://huygens.science.uva.nl/VolcaNoseR2/](https://huygens.science.uva.nl/VolcaNoseR2/)\n\no [https://amsterdamstudygroup.shinyapps.io/VolcaNoseR/](https://amsterdamstudygroup.shinyapps.io/VolcaNoseR/)\n\no [https://goedhart.shinyapps.io/VolcaNoseR/](https://goedhart.shinyapps.io/VolcaNoseR/), while bandwidth lasts\n\nAlternatively, the app can run from R/Rstudio and this is perhaps the best option for loading large files. See instructions below\n\n#### Preparations\nNote that the app depends on several R packages that need to be installed (shiny, ggplot2, dplyr, magrittr, ggrepel, DT, shinycssloaders, RCurl, readxl). \n\nRun this command in R/Rstudio to download and install all the packages (only needs to be done once):\n```\ninstall.packages(\"shiny\", \"tidyverse\", \"ggrepel\", \"DT\", \"shinycssloaders\", \"RCurl\", \"readxl\", \"ggiraph\", \"htmlwidgets\")\n```\no The first option is running it directly from Github. In the command line (in R or Rstudio) type:\n```\nshiny::runGitHub('VolcaNoseR', 'JoachimGoedhart')\n```\no The second option is download the app and to use it offline:\n\n-download the `app.R` and csv files (`Data-Vulcano-plot.csv` and `elife-45916-Cdc42QL_data.csv`) with example data.\n\n-Run RStudio and load `app.R`\n\n-Select 'Run All' (shortcut is command-option-R on a Mac) or click on \"Run App\" (upper right button on the window)\n\nThis should launch a web browser with the Shiny app.\n\n\n### Credits\n\nThere are several Shiny apps for Volcano plots that have served as a source of inspiration:\n\n-[VolcanoR](https://github.com/vovalive/volcanoR)\n\n-[Volcanoshiny](https://github.com/hardingnj/volcanoshiny)\n\n-[VolcanoPlot_shiny_app](https://github.com/stemicha/VolcanoPlot_shiny_app)\n\n\nVolcaNoseR is created and maintained by Joachim Goedhart ([@joachimgoedhart](https://twitter.com/joachimgoedhart))\n\n### Example output\n\nStandard output generated with the example data:\n\n![alt text](https://github.com/JoachimGoedhart/VolcaNoseR/blob/master/VolcaNoseR_example1.png \"Output\")\n\nOutput with user selected annotation of data:\n\n![alt text](https://github.com/JoachimGoedhart/VolcaNoseR/blob/master/VolcaNoseR_example2.png \"Output\")\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FJoachimGoedhart%2FVolcaNoseR","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FJoachimGoedhart%2FVolcaNoseR","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FJoachimGoedhart%2FVolcaNoseR/lists"}