{"id":13942117,"url":"https://github.com/outlierbio/ob-project-template","last_synced_at":"2025-07-20T05:32:08.787Z","repository":{"id":201279288,"uuid":"55527011","full_name":"outlierbio/ob-project-template","owner":"outlierbio","description":"Outlier Bio analysis project template","archived":false,"fork":false,"pushed_at":"2018-01-29T15:13:39.000Z","size":18,"stargazers_count":54,"open_issues_count":0,"forks_count":15,"subscribers_count":4,"default_branch":"master","last_synced_at":"2024-11-27T11:38:51.061Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/outlierbio.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}},"created_at":"2016-04-05T17:12:22.000Z","updated_at":"2024-02-13T22:08:39.000Z","dependencies_parsed_at":null,"dependency_job_id":"ac978773-bd9f-4c2f-8731-6ec91e6f7807","html_url":"https://github.com/outlierbio/ob-project-template","commit_stats":null,"previous_names":["outlierbio/ob-project-template"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/outlierbio/ob-project-template","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/outlierbio%2Fob-project-template","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/outlierbio%2Fob-project-template/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/outlierbio%2Fob-project-template/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/outlierbio%2Fob-project-template/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/outlierbio","download_url":"https://codeload.github.com/outlierbio/ob-project-template/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/outlierbio%2Fob-project-template/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266071519,"owners_count":23871940,"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":"2024-08-08T02:01:42.379Z","updated_at":"2025-07-20T05:32:03.771Z","avatar_url":"https://github.com/outlierbio.png","language":"Jupyter Notebook","funding_links":[],"categories":["Jupyter Notebook"],"sub_categories":[],"readme":"# Outlier Bio project template\n\nThis is a [cookiecutter](https://cookiecutter.readthedocs.io/en/latest/index.html) template for data science projects. It sets up stubs for:\n\n- **standard folder system** with `README.md` descriptions within each folder\n- **Luigi build pipeline**, `build.py`, for downloads and batch preprocessing\n- **Dockerized notebook server** for either Jupyter, RStudio, or RStudio with [Bioconductor](http://www.bioconductor.org/) packages pre-installed. \n- **computational notebook** to run your analysis, either `notebook.ipynb` (if you use Jupyter) or `notebook.Rmd` (if you prefer RMarkdown).\n\nDocker allows you to completely specify your enviroment so your analysis is fully reproducible. Just make sure to add all dependencies (e.g., apt-get for system packages, conda for Python, CRAN or Bioconductor for R) to the Dockerfile and, if applicable, the `install_packages.r` script used by the Dockerfile.\n\nYou can choose the server platform during initiation of the `cookiecutter` script, which will then adjust the Dockerfile accordingly.\n\n## Get started\nFrom a terminal, change to the directory you want to hold the project folder, and run cookiecutter:\n\n\t`$ cookiecutter /path/to/ob-project-template`\n\t\nFill in the prompts (your name and email, project name and description, and the flavor of notebook platform) and it will be created for you! Be sure to double-check the auto-generated project slug and fix it if necessary–this will be the name of the folder.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Foutlierbio%2Fob-project-template","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Foutlierbio%2Fob-project-template","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Foutlierbio%2Fob-project-template/lists"}