{"id":13951606,"url":"https://github.com/Appsilon/shiny.molstar","last_synced_at":"2025-07-20T15:31:28.757Z","repository":{"id":178961097,"uuid":"601573708","full_name":"Appsilon/shiny.molstar","owner":"Appsilon","description":"R Shiny wrapper for Mol* (/'molstar/) - A visualization toolkit of large-scale molecular data","archived":false,"fork":false,"pushed_at":"2024-10-31T23:28:52.000Z","size":14986,"stargazers_count":17,"open_issues_count":6,"forks_count":1,"subscribers_count":15,"default_branch":"main","last_synced_at":"2024-11-01T00:22:50.859Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://appsilon.github.io/shiny.molstar/","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/Appsilon.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE","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":"2023-02-14T11:04:00.000Z","updated_at":"2024-10-11T14:32:32.000Z","dependencies_parsed_at":"2023-10-12T05:17:36.951Z","dependency_job_id":"3170f3ea-3105-4955-adfa-9128a0db440c","html_url":"https://github.com/Appsilon/shiny.molstar","commit_stats":null,"previous_names":["appsilon/shiny.molstar"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Appsilon%2Fshiny.molstar","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Appsilon%2Fshiny.molstar/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Appsilon%2Fshiny.molstar/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Appsilon%2Fshiny.molstar/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Appsilon","download_url":"https://codeload.github.com/Appsilon/shiny.molstar/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":226809040,"owners_count":17685496,"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":[],"created_at":"2024-08-08T07:00:38.466Z","updated_at":"2024-11-27T19:30:43.800Z","avatar_url":"https://github.com/Appsilon.png","language":"R","funding_links":[],"categories":["Visualization"],"sub_categories":["Biological Data"],"readme":"# shiny.molstar \u003ca href=\"https://appsilon.github.io/shiny.molstar/\"\u003e\u003cimg src=\"man/figures/logo.svg\" align=\"right\" alt=\"data.validator logo\" style=\"height: 140px;\"\u003e\u003c/a\u003e\n\n\u003e _R Shiny wrapper for Mol* (/'molstar/) - A visualization toolkit of large-scale molecular data_\n\n\u003c!-- badges: start --\u003e\n[![R-CMD-checks](https://github.com/Appsilon/shiny.molstar/actions/workflows/ci.yml/badge.svg)](https://github.com/Appsilon/shiny.molstar/actions/workflows/ci.yml)\n\u003c!-- badges: end --\u003e\n\nBased on [Mol*](https://molstar.org) (/'molstar/) and powered by [shiny.react](https://appsilon.github.io/shiny.react/)\n\nWe created a R Shiny wrapper based on [shiny.react](https://appsilon.github.io/shiny.react/) and [molstar-react](https://www.npmjs.com/package/molstar-react) _(node.js library)_ that gives all the powerful tools of Mol* open-source toolkit for visualization and analysis of large-scale molecular data.\n\nThis package exports three new components that can be used in a Shiny application.\n\n* `Molstar` creates a Molstar visualization of a protein using an URL to a valid filetype supported by Molstar or a \"Protein Data Bank\" id _(pdbId)_. See more below for available databases to find a valid `pdbId`.\n* `AlphaFoldMolstar` similar to the Molstar component, but uses the UniProt id in the AlphaFold database to display the protein.\n* `AlphaFoldDetails` creates a component that retrieves details of an AlphaFold protein id _(title, download links and a Predict Aligned Error image)_\n\n### How to find a valid id or url?\n\nA valid `pdbId` can be found in public databases such as:\n\n* [EMBL-EBI database](https://www.ebi.ac.uk/pdbe/entry/search/index/)\n* [RSCB.org](https://www.rcsb.org/)\n\nThe `uniProtId` can be found in any of the AlphaFold databases:\n\n* [AlphaFold.com](https://alphafold.com/)\n\n## Getting started\n\nTo install the package, run:\n\n```{R}\nremotes::install_github(\"Appsilon/shiny.molstar\")\n```\n\nTake a look at basic [example app](https://github.com/Appsilon/shiny.molstar/blob/main/inst/examples/Minimal.R) to start working with shiny.molstar.\n\nTo learn about the Mol* language, follow the [Viewer documentation](https://molstar.org/viewer-docs/).\n\n## Examples\n\nA good way to learn more is to look at the examples. Once you install the library, you can run them with `shiny.molstar::runExample` function.\n\n```{R}\nshiny.molstar::runExample(\"FullPage\")\nshiny.molstar::runExample(\"Minimal\")\nshiny.molstar::runExample(\"AlphaFold\")\nshiny.molstar::runExample(\"AlphaFoldDetails\")\n```\n\n### Full page example\n\nCreating a full page viewer on a sample molecule _(example also available at `inst/examples/FullPage.R`)_\n\n```{R}\nlibrary(shiny)\nlibrary(shiny.molstar)\n\nshinyApp(\n  ui = tagList(\n    tags$style(HTML(\"html, body { margin: 0; }\")),\n    Molstar(\n      pdbId = \"1LOL\",\n      useInterface = TRUE,\n      showControls = TRUE,\n      showAxis = TRUE\n    )\n  ),\n  server = function(input, output) {\n  }\n)\n```\n\n![Full page example](man/figures/example.gif)\n\n### Using AlphaFold database and details\n\nRunning an example from the package _(located at `inst/examples/AlphaFoldDetails.R`)_.\n\nYou can click on the button on the bottom of the example to get the minimal code to reproduce the same Shiny application _(unstyled and without the footer)_.\n\n```{R}\nshiny.molstar::runExample(\"AlphaFoldDetails\")\n```\n\n![AlphaFold with details](man/figures/example2.gif)\n\n## Appsilon\n\n\u003cimg src=\"https://avatars0.githubusercontent.com/u/6096772\" align=\"right\" alt=\"\" width=\"6%\" /\u003e\n\nAppsilon is a **Posit (formerly RStudio) Full Service Certified Partner**.\u003cbr/\u003e\nLearn more at [appsilon.com](https://appsilon.com).\n\nGet in touch [opensource@appsilon.com](mailto:opensource@appsilon.com)\n\nExplore the [Rhinoverse](https://rhinoverse.dev) - a family of R packages built around [Rhino](https://appsilon.github.io/rhino/)!\n\n\u003ca href = \"https://appsilon.com/careers/\" target=\"_blank\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/Appsilon/website-cdn/gh-pages/WeAreHiring1.png\" alt=\"We are hiring!\"/\u003e\u003c/a\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FAppsilon%2Fshiny.molstar","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FAppsilon%2Fshiny.molstar","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FAppsilon%2Fshiny.molstar/lists"}