{"id":29303558,"url":"https://github.com/scverse/scverse-tutorials","last_synced_at":"2025-07-07T01:09:06.924Z","repository":{"id":64311427,"uuid":"572408536","full_name":"scverse/scverse-tutorials","owner":"scverse","description":"Tutorials for learning scverse","archived":false,"fork":false,"pushed_at":"2025-07-01T17:40:47.000Z","size":55513,"stargazers_count":16,"open_issues_count":17,"forks_count":13,"subscribers_count":7,"default_branch":"main","last_synced_at":"2025-07-01T18:36:06.731Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://scverse-tutorials.readthedocs.io/en/latest/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/scverse.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.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,"zenodo":null}},"created_at":"2022-11-30T07:57:42.000Z","updated_at":"2025-07-01T17:40:50.000Z","dependencies_parsed_at":"2025-03-24T18:36:49.004Z","dependency_job_id":"9ba68ca8-fa6c-4e26-8183-f322335e35c0","html_url":"https://github.com/scverse/scverse-tutorials","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/scverse/scverse-tutorials","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fscverse-tutorials","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fscverse-tutorials/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fscverse-tutorials/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fscverse-tutorials/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/scverse","download_url":"https://codeload.github.com/scverse/scverse-tutorials/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fscverse-tutorials/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263996091,"owners_count":23541402,"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":"2025-07-07T01:09:01.808Z","updated_at":"2025-07-07T01:09:06.919Z","avatar_url":"https://github.com/scverse.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# scverse tutorials\n\n[![Documentation][badge-docs]][link-docs]\n\nOn [scverse.org/learn](https://scverse.org/learn), we aim at providing a comprehensive overview of analyses that can be\nperformed with scverse core and ecosystem packages.\n\nTo this end, this repository contains\n\n- a registry for tutorials listed on [scverse.org/learn](https://scverse.org/learn) (see `tutorial-registry`)\n- shared tutorials that complement more specific tutorials provided by invidiual [core](https://scverse.org/packages/)\n  and [ecosystem](https://scverse.org/packages/#ecosystem) packages (see `docs`)\n\n## Adding tutorials\n\nIf you believe a tutorial should be added to `scverse.org/learn`, please open an issue. We will discuss the request\nin the next [open community meeting](https://hackmd.io/VfVLKb3ETGKN2j_7tn8ZJQ?view) and potentially suggest\nimprovements.\n\nTo be added to our website, tutorials must fulfill at least the following requirements:\n\n- all featured packages must be scverse [core](https://scverse.org/packages/#core-packages) or\n  [approved ecosystem packages](https://scverse.org/packages/#ecosystem). This does not apply to packages that are not\n  specific to omics data analysis (e.g. pandas, seaborn).\n- the notebook author agrees to maintain the tutorial in the future and is reachable via [zulip](https://scverse.zulipchat.com).\n- the notebook contains a backlink to [scverse.org/learn](https://scverse.org/learn)\n- the notebook is self-contained: All required example data is downloaded as part of the tutorial\n\nYou can easily check your changes to tutorials or the registry locally:\n\n```shell\nhatch run docs:build  # for tutorial notebooks\nhatch run registry:validate  # for the tutorials registry\n```\n\n## Structure of external tutorials\n\nWhile we do not mandate a specific structure for tutorials,\na good tutorial typically comprises the following sections:\n\n1. **General header**: The tutorial should have a general header that corresponds to the analysis.\n2. **Brief introduction**: The tutorial should introduce the package, the analysis motivation and potentially biological background.\n3. **Requirements to run the notebook**: Special computational requirements like memory or GPUs should be specified. Any required input from other notebooks should also be listed here.\n4. **Package imports**: All required packages should now be imported.\n5. **General setup**: General settings such as plotting settings or ignored warnings should be set up here.\n6. **Data loading**: Any required datasets should be loaded here. Ideally with stable links.\n7. **Data preprocessing**: Any data preprocessing should be done here. Depending on the method this step can be skipped.\n8. **Package specific tutorial**: The tutorial for the package should contain a healthy mix of text and code to guide the user through the analysis.\n9. **Link to other important tutorials/packages/sources of information**: Link to any other tutorials that might be of interest or the corresponding https://sc-best-practices.org chapter.\n10. **References**: Any referenced papers should show up in references section.\n11. **Acknowledgements**: All contributing authors and experts should be named.\n\n[link-docs]: https://scverse-tutorials.readthedocs.io/en/latest/\n[badge-docs]: https://img.shields.io/readthedocs/scverse-tutorials\n[//]: # \"numfocus-fiscal-sponsor-attribution\"\n\nscverse-tutorials is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).\nIf you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.\n\n\u003cdiv align=\"center\"\u003e\n\u003ca href=\"https://numfocus.org/project/scverse\"\u003e\n  \u003cimg\n    src=\"https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png\"\n    width=\"200\"\n  \u003e\n\u003c/a\u003e\n\u003c/div\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fscverse-tutorials","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscverse%2Fscverse-tutorials","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fscverse-tutorials/lists"}