# Tutorials

The documentation comes in three tiers. **Tutorials** teach a full biological workflow end to end, from a raw
object to an interpreted result. **Examples** are short, focused how-to recipes for one task, such as reading a
particular input format. **Pitfalls** show what goes wrong in image-based profiling and how to detect it before it
reaches a conclusion.

Start with the overview, which runs the whole workflow on one page and links to the page that covers each step.

```{toctree}
:maxdepth: 1
:caption: Tutorials — start here

overview
```

```{toctree}
:maxdepth: 1
:caption: Tutorials — preparing profiles

profiles/quality_control
profiles/normalize_and_select
profiles/artifacts
profiles/screen_quality
```

```{toctree}
:maxdepth: 1
:caption: Tutorials — compound screens

compounds/hits
compounds/mechanism_of_action
compounds/enrichment
compounds/dose_response
```

```{toctree}
:maxdepth: 1
:caption: Tutorials — genetic screens

genetics/crispr
genetics/interpreting_a_screen
```

```{toctree}
:maxdepth: 1
:caption: Tutorials — single cells

single_cells/heterogeneity
```

```{toctree}
:maxdepth: 1
:caption: Tutorials — across laboratories

multisite/cross_laboratory
multisite/learned_embeddings
```

```{toctree}
:maxdepth: 1
:caption: Examples — bringing data in

data/cellprofiler
data/profiles
data/embeddings
data/images
```

```{toctree}
:maxdepth: 1
:caption: Pitfalls

pitfalls/index
phenotypes/which_features_moved
```