{"id":18733485,"url":"https://github.com/insightsengineering/biomarker-catalog","last_synced_at":"2025-11-14T04:30:17.229Z","repository":{"id":154984148,"uuid":"617055285","full_name":"insightsengineering/biomarker-catalog","owner":"insightsengineering","description":"Biomarker Analysis Templates of Tables And Graphs 📊","archived":false,"fork":false,"pushed_at":"2025-02-12T17:27:31.000Z","size":99271,"stargazers_count":9,"open_issues_count":3,"forks_count":2,"subscribers_count":9,"default_branch":"main","last_synced_at":"2025-02-12T18:35:03.264Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://insightsengineering.github.io/biomarker-catalog/","language":"SCSS","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/insightsengineering.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,"dei":null,"publiccode":null,"codemeta":null},"funding":{"custom":["https://pharmaverse.org"]}},"created_at":"2023-03-21T16:00:25.000Z","updated_at":"2025-02-04T09:46:36.000Z","dependencies_parsed_at":"2023-07-14T19:07:17.197Z","dependency_job_id":"b7ce4fc4-8aec-4b64-8205-f28ad21f1fad","html_url":"https://github.com/insightsengineering/biomarker-catalog","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/insightsengineering%2Fbiomarker-catalog","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/insightsengineering%2Fbiomarker-catalog/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/insightsengineering%2Fbiomarker-catalog/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/insightsengineering%2Fbiomarker-catalog/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/insightsengineering","download_url":"https://codeload.github.com/insightsengineering/biomarker-catalog/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239605124,"owners_count":19666998,"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":"2024-11-07T15:09:55.934Z","updated_at":"2025-11-14T04:30:17.189Z","avatar_url":"https://github.com/insightsengineering.png","language":"SCSS","funding_links":["https://pharmaverse.org"],"categories":[],"sub_categories":[],"readme":"# Biomarker Analysis Catalog\n\nCatalog for tables and graphs produced by Statistical Engineering products.\n\n## Architecture\n\nThis repository follows a very straightforward architecture.\n\n```mermaid\nsequenceDiagram\n    autonumber\n    Author-\u003e\u003eRepo: Creates content + pushes updates\n    Repo-\u003e\u003eGitHub Actions: Triggers builds\n    GitHub Actions-\u003e\u003eGitHub Pages: Publishes the catalog\n    Analyst-\u003e\u003eGitHub Pages: Refers to catalog\n```\n\n## Technology\n\n- Dependency management: [`staged.dependencies`](https://openpharma.github.io/staged.dependencies/) for installing dependencies\n- Building and rendering: [`Quarto`](https://quarto.org/)\n- Publishing: [`GitHub Actions`](https://docs.github.com/en/actions)\n- Hosting: [`GitHub Pages`](https://pages.github.com/)\n\n## Development\n\nThis repository is based on the [Quarto books](https://quarto.org/docs/books/) framework.\n\nAs a pre-requsite, you need to [install Quarto](https://quarto.org/docs/get-started/) and also [install and configure staged.dependencies](https://github.com/openpharma/staged.dependencies#usage).\n\nYou can install dependencies simply by running the following in an R session:\n\n```R\n# Assuming:\n# 1. Your current working directory is the same as the project directory\n# 2. You have set up your GITHUB_PAT environment variable\noptions(\n  staged.dependencies.token_mapping = c(\n    \"https://github.com\" = \"GITHUB_PAT\"\n  )\n)\nlibrary(staged.dependencies)\nx \u003c- dependency_table(project = \".\", verbose = 1)\ninstall_deps(x, verbose = 1, install_project = FALSE)\n```\n\nThen, install this \"package\" (because it's not really a package, but it emulates a package as it has a `DESCRIPTION` file from which metadata is inferred):\n\n```shell\nR CMD INSTALL .\n```\n\nYou'll see that files under [tables](tables) and [graphs](graphs) are in a `.qmd` file format, which translates to a **q**uarto **m**ark**d**own format. Note that the format is _almost exactly_ the same as Rmarkdown, with some minor differences, so you would write content within those files exactly as you would write Rmarkdown.\n\nIf you are adding a new table or graph in the form a a new `qmd` file, then you will also need to update the index in the [_quarto.yml](_quarto.yml) file with the new file name.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finsightsengineering%2Fbiomarker-catalog","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Finsightsengineering%2Fbiomarker-catalog","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finsightsengineering%2Fbiomarker-catalog/lists"}