```{include} ../README.md

```

```{toctree}
:caption: Usage
:name: usage
:hidden:
:maxdepth: 1

getting_started/index.md
principles/index.md
```


```{toctree}
:caption: Modules
:name: modules
:hidden:
:maxdepth: 2

modules/index_data_preparation
modules/index_integration
modules/index_downstream
modules/index_helpers
```

```{toctree}
:caption: Tutorials
:name: tutorials
:hidden:
:maxdepth: 1

workflows/qc
workflows/batch_analysis
workflows/integration
workflows/metrics
workflows/clustering
workflows/label_harmonization
```