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format the decision tree
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dbdimitrov committed Jul 12, 2024
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A set of extensive vignettes can be found in the [LIANA+ documentation](https://liana-py.readthedocs.io/en/latest/).

## Decision Tree

C1: Does the data contain spatial coordinates?
├── Yes
│ ├── Q: Bivariate or unsupervised, multi-variate, and multi-view analysis?
│ ├── Bivariate:
│ │ ├── Q: Are you interested in identifying the subregions of interactions (i.e., local interactions)?
│ │ ├── Yes -> Check the [**Local** Bivariate Metrics](https://liana-py.readthedocs.io/en/latest/notebooks/bivariate.html#Bivariate-Ligand-Receptor-Relationships)
│ │ ├── No -> Check the [**Global** Bivariate Metrics](https://liana-py.readthedocs.io/en/latest/notebooks/bivariate.html#Bivariate-Ligand-Receptor-Relationships)
│ └── Unsupervised: [Multi-view learning](https://liana-py.readthedocs.io/en/latest/notebooks/misty.html)
└── No
├── Q: Are you interested in Comparing CCC across Samples?
├── Yes
│ ├── Q: Are you interested in a specific contrast?
│ │ ├── Yes -> [Differential Contrasts and Downstream Signalling](https://liana-py.readthedocs.io/en/latest/notebooks/targeted.html)
│ │ └── No -> Unsupervised Cross-conditional LR inference with [MOFA+](https://liana-py.readthedocs.io/en/latest/notebooks/mofatalk.html) or [Tensor-cell2cell](https://liana-py.readthedocs.io/en/latest/notebooks/liana_c2c.html)
└── No -> [Steady-state Ligand-Receptor inference](https://liana-py.readthedocs.io/en/latest/notebooks/basic_usage.html)

Is your data Multi-modal?
├── Spatial: [Integrating Multi-Modal Spatially-Resolved Technologies](https://liana-py.readthedocs.io/en/latest/notebooks/sma.html)
└── Non-Spatial: [Integrating Multi-Modal Single-Cell Technologies](https://liana-py.readthedocs.io/en/latest/notebooks/sc_multi.html)

### Q: Does the data contain spatial coordinates?
#### Yes
- **Q: Bivariate or unsupervised, multi-variate, and multi-view analysis?**
- **Bivariate:**
- **Q: Are you interested in identifying the subregions of interactions (i.e., local interactions)?**
- **Yes:** Check the [**Local** Bivariate Metrics](https://liana-py.readthedocs.io/en/latest/notebooks/bivariate.html#Bivariate-Ligand-Receptor-Relationships)
- **No:** Check the [**Global** Bivariate Metrics](https://liana-py.readthedocs.io/en/latest/notebooks/bivariate.html#Bivariate-Ligand-Receptor-Relationships)
- **Unsupervised:** [Multi-view learning](https://liana-py.readthedocs.io/en/latest/notebooks/misty.html)

#### No
- **Q: Are you interested in comparing CCC across samples?**
- **Yes:**
- **Q: Are you interested in a specific contrast?**
- **Yes:** [Differential Contrasts and Downstream Signalling](https://liana-py.readthedocs.io/en/latest/notebooks/targeted.html)
- **No:** Unsupervised Cross-conditional LR inference with [MOFA+](https://liana-py.readthedocs.io/en/latest/notebooks/mofatalk.html) or [Tensor-cell2cell](https://liana-py.readthedocs.io/en/latest/notebooks/liana_c2c.html)
- **No:** [Steady-state Ligand-Receptor inference](https://liana-py.readthedocs.io/en/latest/notebooks/basic_usage.html)

### Is your data Multi-modal?
- **Spatial:** [Integrating Multi-Modal Spatially-Resolved Technologies](https://liana-py.readthedocs.io/en/latest/notebooks/sma.html)
- **Non-Spatial:** [Integrating Multi-Modal Single-Cell Technologies](https://liana-py.readthedocs.io/en/latest/notebooks/sc_multi.html)

## API
For further information please check LIANA's [API documentation](https://liana-py.readthedocs.io/en/latest/api.html).
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