{"id":14067878,"url":"https://github.com/systemPipeR/systemPipeShiny","last_synced_at":"2025-07-30T02:32:10.833Z","repository":{"id":39788928,"uuid":"241477718","full_name":"systemPipeR/systemPipeShiny","owner":"systemPipeR","description":"A Shiny framework for workflow management and data visualization","archived":false,"fork":false,"pushed_at":"2023-10-16T17:32:43.000Z","size":27391,"stargazers_count":34,"open_issues_count":0,"forks_count":7,"subscribers_count":5,"default_branch":"devel","last_synced_at":"2024-12-01T02:51:48.696Z","etag":null,"topics":["bioconductor","bioconductor-package","data-visualization","r","shiny","systempiper"],"latest_commit_sha":null,"homepage":"https://systempipe.org/sps/","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/systemPipeR.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":"2020-02-18T22:05:59.000Z","updated_at":"2024-10-15T06:59:21.000Z","dependencies_parsed_at":"2024-01-06T14:50:09.238Z","dependency_job_id":null,"html_url":"https://github.com/systemPipeR/systemPipeShiny","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/systemPipeR%2FsystemPipeShiny","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/systemPipeR%2FsystemPipeShiny/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/systemPipeR%2FsystemPipeShiny/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/systemPipeR%2FsystemPipeShiny/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/systemPipeR","download_url":"https://codeload.github.com/systemPipeR/systemPipeShiny/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":228075633,"owners_count":17865508,"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":["bioconductor","bioconductor-package","data-visualization","r","shiny","systempiper"],"created_at":"2024-08-13T07:05:49.591Z","updated_at":"2024-12-04T08:31:19.003Z","avatar_url":"https://github.com/systemPipeR.png","language":"R","readme":"\n# systemPipeShiny \u003cimg src=\"https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/images/sps_small.png?raw=true\" align=\"right\" height=\"139\" /\u003e\n\n\u003c!-- badges: start --\u003e\n![R-CMD-check](https://github.com/systemPipeR/systemPipeShiny/workflows/R-CMD-check/badge.svg)\n\u003c!-- badges: end --\u003e\n\n`systemPipeShiny`(SPS) a Shiny-based R/Bioconductor package that extends the widely used \n[systemPipeR](http://www.bioconductor.org/packages/release/bioc/html/systemPipeR.html) workflow \nenvironment with data visualization and a versatile graphical user interface. \nSPS can work as a general framework to build custom web apps on data analysis and visualization.\nBesides, SPS provides many developer tools that are distributed as [separate packages](#other-packages-in-systempipeshiny). \n\n## 4 minutes quick overview\nYou need to unmuted it to hear the sound. \n\nhttps://user-images.githubusercontent.com/35240440/199619635-97b6a8bd-40b1-4a64-8309-a8622e099d97.mp4\n\n![design](https://systempipe.org/sps/img/sps_structure.png)\n\n## Demos\nSPS has provided a variety of options to change how it work. Here are some examples.\n\n| Type and link| option changed | notes |\n| --- | --- | --- |\n| [Default full installation](https://tgirke.shinyapps.io/systemPipeShiny/) | [See installation](#installation) | full app, may take longer (~15s) to load |\n| [Minimum installation](https://tgirke.shinyapps.io/systemPipeShiny_min/) | [See installation](#installation) | no modules installed |\n| [Login enabled](https://tgirke.shinyapps.io/systemPipeShiny_loading/) | `login_screen = TRUE; login_theme = \"empty\"` | no modules installed |\n| [Login and login themes](https://tgirke.shinyapps.io/systemPipeShiny_loading_theme/) | `login_screen = TRUE; login_theme = \"random\"` | no modules installed |\n| [App admin page](https://tgirke.shinyapps.io/systemPipeShiny_loading/?admin) | `admin_page = TRUE` | use the link or simply add \"?admin\" to the end of URL of any demos |\n\nFor the login required demos, the app account name is **\"user\"** password **\"user\"**.\n\nFor the admin login, account name **\"admin\"**, password **\"admin\"**.\n\n**Please DO NOT delete or change password when you are trying the admin features.**\nAlthough _shinyapps.io_ will reset the app once a while, this will affect other people \nwho are viewing the demo simultaneously. \n\n### Rstudio Cloud\nThere is an [Rstudio Cloud project](https://rstudio.cloud/project/2493103) instance \nthat you can also play with. You need to create a free new account. Two Bioconductor\nrelated modules - workflow \u0026 RNAseq are not installed. They require more than 1GB \nRAM to install and to run which is beyond the limit of a free account. \n\n### Docker\nUse [systempipe_docker](https://github.com/systemPipeR/systempipe_docker) for instructions.\n\n## [Documents](https://systempipe.org/sps/)\n\nTo see all the details of SPS, read the user manual on [our website](https://systempipe.org/sps/).\n\n## Installation\n\n### Full\n\n``` r\nif (!requireNamespace(\"BiocManager\", quietly=TRUE))\n    install.packages(\"BiocManager\")\nBiocManager::install(\"systemPipeShiny\", dependencies=TRUE)\n\n```\nThis will install **all** required packages including suggested packages that \nare required by the core modules. Be aware, it will take quite some time if you \nare installing on Linux where only source installation is available. Windows and Mac\nbinary installations will be much faster. \n\n### Minimum\n\nTo install the package, please use the `BiocManager::install` command:\n\n``` r\nif (!requireNamespace(\"BiocManager\", quietly=TRUE))\n    install.packages(\"BiocManager\")\nBiocManager::install(\"systemPipeShiny\")\n\n```\n\nBy the minimum installation, all the 3 core modules are **not** installed. You \ncan still start the app, and when you start the app and click on these modules, \nit will tell to enable these modules, what packages to install and what \ncommand you need to run. \nJust follow the instructions. Install as you need.\n\n### Most recent \n\nTo obtain the most recent updates immediately, one can install it directly from \n[GitHub](https://github.com/systemPipeR/systemPipeShiny) as follow:\n\n``` r\nif (!requireNamespace(\"remotes\", quietly=TRUE))\n    install.packages(\"remotes\")\nremotes::install(\"systemPipeR/systemPipeShiny\", dependencies=TRUE)\n```\n\nSimilarly, `remotes::install(\"systemPipeR/systemPipeShiny\")` for the minimum develop\nversion. \n\n### Linux\n\nIf you are on Linux, you may also need the following system dependencies  **before installing SPS**.\nDifferent distributions \nmay have different commands, but the following commands are examples for Ubuntu:\n\n```bash\nsudo apt-get install -y libicu-dev\nsudo apt-get install -y pandoc\nsudo apt-get install -y zlib1g-dev\nsudo apt-get install -y libcurl4-openssl-dev\nsudo apt-get install -y libssl-dev      \nsudo apt-get install -y make\n```\n## Quick start\n\nThis is a basic example which shows how to use `systempipeShiny` package:\n\n``` r\n## Imports the library\nlibrary(systemPipeShiny)\n## Creates the project directory\nspsInit()\n```\n\nBy default, a project folder is created and named as `SPS_`+`DATE`. \nThis project folder provides all the necessary files to launch the application. \nIf you are using Rstudio, `global.R` file will be opened automatically and this is \nthe only file you may need to make custom changes if there is any.\n\nClick the green \"Run App\" button in Rstudio if you are on the `global.R` file or \nrun following in console to start the app. \n\n``` r\n## Launching the interface\nshiny::runApp()\n```\n\n### [options](https://systempipe.org/sps/adv_features/config/#app-options)\nChange some of the [options](https://systempipe.org/sps/adv_features/config/#app-options)\nlisted in `global.R` will change how the app behave, for example, modules to load,\ntitle, logo, whether to apply user authentication, and more ...\n\n## Other packages in systemPipeShiny\n\n| Package | Description | Documents | Function reference | Demo |\n| --- | --- | --- | :---: | --- |\n|\u003cimg src=\"https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/images/sps_small.png?raw=true\" align=\"right\" height=\"30\" width=\"30\"/\u003e[systemPipeShiny](https://github.com/systemPipeR/systemPipeShiny) | SPS main package |[website](https://systempipe.org/sps/)|[link](https://systempipe.org/sps/funcs/sps/reference/)  | [demo](https://tgirke.shinyapps.io/systemPipeShiny/)|\n|\u003cimg src=\"https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/images/spscomps.png?raw=true\" align=\"right\" height=\"30\" width=\"30\" /\u003e[spsComps](https://github.com/lz100/spsComps) | SPS UI and server components |[website](https://systempipe.org/sps/dev/spscomps/)|[link](https://systempipe.org/sps/funcs/spscomps/reference/)  | [demo](https://lezhang.shinyapps.io/spsComps)|\n|\u003cimg src=\"https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/images/drawer.png?raw=true\" align=\"right\" height=\"30\" width=\"30\" /\u003e[drawer](https://github.com/lz100/drawer) | SPS interactive image editing tool |[website](https://systempipe.org/sps/dev/drawer/)|[link](https://systempipe.org/sps/funcs/drawer/reference/)  | [demo](https://lezhang.shinyapps.io/drawer)|\n|\u003cimg src=\"https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/images/spsutil.png?raw=true\" align=\"right\" height=\"30\" width=\"30\" /\u003e[spsUtil](https://github.com/lz100/spsUtil) | SPS utility functions |[website](https://systempipe.org/sps/dev/spsutil/)|[link](https://systempipe.org/sps/funcs/spsutil/reference/)  | NA|\n\n\n## More Tutorials \n\u003cdetails\u003e\n    \u003csummary\u003eExpand\u003c/summary\u003e\n\nYou need to unmuted it to hear the sound. \n\n### Workflow Module\nhttps://user-images.githubusercontent.com/35240440/199857935-64267b1a-fbb2-4a9c-a460-bafcf2f6e95a.mp4\n\n### RNAseq Module\nhttps://user-images.githubusercontent.com/35240440/199857988-525e4f50-df90-4bb5-bb3e-41142182ed83.mp4\n\n### Quick ggplot Module\nhttps://user-images.githubusercontent.com/35240440/199858014-02af7c97-daf1-4728-a9f5-cb0d4d256bf9.mp4\n\n### Canvas Tool\nhttps://user-images.githubusercontent.com/35240440/199858040-9d5443ff-a0ef-4bbe-b4e7-93aa442e64fa.mp4\n\n\u003c/details\u003e\n\n## Screenshots of SPS\n\u003cdetails\u003e\n    \u003csummary\u003eExpand\u003c/summary\u003e\n    \n##### Full app\n![sps](https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/main_app.png?raw=true)\n\n##### Loading screens\n![loading screens](https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/loading_theme.gif?raw=true)\n\n##### Workflow module\n\n![WF](https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/wf_main.png?raw=true)\n\n##### Workflow Execution\n![WF run](https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/wf_run.png?raw=true)\n\n##### RNASeq module\n![RNASeq module](https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/rnaseq_deg.png?raw=true)\n\n![RNASeq module](https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/rnaseq_heatmap.png?raw=true)\n\n##### Canvas \n![canvas](https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/canvas.png?raw=true)\n\n##### Admin\n![Admin](https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/admin_login.png?raw=true)\n\n![Admin](https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/admin_server_info.png?raw=true)\n\n![Admin](https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/admin_user_control.png?raw=true)\n\n##### Debugging\n![Debugging](https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/logging.png?raw=true)\n\n\u003c/details\u003e\n\n## Contact \u0026 contributions\n \nPlease use https://github.com/systemPipeR/systemPipeShiny/issues for reporting bugs, \nissues or for suggesting new features to be implemented.\n\nWe'd love to hear from all users and developers. Submit your pull request if you \nhave new thoughts or improvements. \n\n\n","funding_links":[],"categories":["Tools","R"],"sub_categories":["Packages"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FsystemPipeR%2FsystemPipeShiny","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FsystemPipeR%2FsystemPipeShiny","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FsystemPipeR%2FsystemPipeShiny/lists"}