https://github.com/scverse/scverse-tutorials
Tutorials for learning scverse
https://github.com/scverse/scverse-tutorials
Last synced: 11 months ago
JSON representation
Tutorials for learning scverse
- Host: GitHub
- URL: https://github.com/scverse/scverse-tutorials
- Owner: scverse
- License: bsd-3-clause
- Created: 2022-11-30T07:57:42.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2025-07-01T17:40:47.000Z (11 months ago)
- Last Synced: 2025-07-01T18:36:06.731Z (11 months ago)
- Language: Python
- Homepage: https://scverse-tutorials.readthedocs.io/en/latest/
- Size: 52.9 MB
- Stars: 16
- Watchers: 7
- Forks: 13
- Open Issues: 17
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
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README
# scverse tutorials
[![Documentation][badge-docs]][link-docs]
On [scverse.org/learn](https://scverse.org/learn), we aim at providing a comprehensive overview of analyses that can be
performed with scverse core and ecosystem packages.
To this end, this repository contains
- a registry for tutorials listed on [scverse.org/learn](https://scverse.org/learn) (see `tutorial-registry`)
- shared tutorials that complement more specific tutorials provided by invidiual [core](https://scverse.org/packages/)
and [ecosystem](https://scverse.org/packages/#ecosystem) packages (see `docs`)
## Adding tutorials
If you believe a tutorial should be added to `scverse.org/learn`, please open an issue. We will discuss the request
in the next [open community meeting](https://hackmd.io/VfVLKb3ETGKN2j_7tn8ZJQ?view) and potentially suggest
improvements.
To be added to our website, tutorials must fulfill at least the following requirements:
- all featured packages must be scverse [core](https://scverse.org/packages/#core-packages) or
[approved ecosystem packages](https://scverse.org/packages/#ecosystem). This does not apply to packages that are not
specific to omics data analysis (e.g. pandas, seaborn).
- the notebook author agrees to maintain the tutorial in the future and is reachable via [zulip](https://scverse.zulipchat.com).
- the notebook contains a backlink to [scverse.org/learn](https://scverse.org/learn)
- the notebook is self-contained: All required example data is downloaded as part of the tutorial
You can easily check your changes to tutorials or the registry locally:
```shell
hatch run docs:build # for tutorial notebooks
hatch run registry:validate # for the tutorials registry
```
## Structure of external tutorials
While we do not mandate a specific structure for tutorials,
a good tutorial typically comprises the following sections:
1. **General header**: The tutorial should have a general header that corresponds to the analysis.
2. **Brief introduction**: The tutorial should introduce the package, the analysis motivation and potentially biological background.
3. **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.
4. **Package imports**: All required packages should now be imported.
5. **General setup**: General settings such as plotting settings or ignored warnings should be set up here.
6. **Data loading**: Any required datasets should be loaded here. Ideally with stable links.
7. **Data preprocessing**: Any data preprocessing should be done here. Depending on the method this step can be skipped.
8. **Package specific tutorial**: The tutorial for the package should contain a healthy mix of text and code to guide the user through the analysis.
9. **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.
10. **References**: Any referenced papers should show up in references section.
11. **Acknowledgements**: All contributing authors and experts should be named.
[link-docs]: https://scverse-tutorials.readthedocs.io/en/latest/
[badge-docs]: https://img.shields.io/readthedocs/scverse-tutorials
[//]: # "numfocus-fiscal-sponsor-attribution"
scverse-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/).
If 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.
