# Tutorials

```{eval-rst}
For beginners, we recommend using the command-line interface (CLI), which automates parts of the workflow and generates many outputs for downstream analysis.
    1. `CLI factorization <tutorials/cli-factorization.md>`
    2. `CLI integration <tutorials/cli-integration.md>`
    3. `CLI gene set analysis <tutorials/cli-geneset-analysis.md>`

For advanced users, we recommend the using Python, which provides better control over the analysis parameters and plotting, as well as integration with other APIs and in-memory data structures. The following tutorials demonstrate how to follow a similar workflow as the CLI tutorials above:
    1. `Python factorization <tutorials/python-factorization.ipynb>`
    2. `Python integration <tutorials/python-integration.ipynb>`

```

```{toctree}
:maxdepth: 1
tutorials/cli-factorization.md
tutorials/cli-integration.md
tutorials/cli-integration-configuration.md
tutorials/cli-geneset-analysis.md
tutorials/python-factorization.ipynb
tutorials/python-integration.ipynb
```