Metadata-Version: 2.4
Name: liana
Version: 1.6.0
Summary: LIANA+: a one-stop-shop framework for cell-cell communication
Project-URL: Documentation, https://liana.readthedocs.io/
Project-URL: Homepage, https://liana-py.readthedocs.io
Project-URL: Source, https://github.com/saezlab/liana-py
Author: Daniel Dimitrov, Philipp Sven Lars Schäfer, Elias Farr, Pablo Rodriguez-Mier, Sebastian Lobentanzer, Pau Badia-i-Mompel, Aurelien Dugourd, Jovan Tanevski, Ricardo Omar Ramirez Flores, Julio Saez-Rodriguez
Maintainer-email: Daniel Dimitrov <daniel.dimitrov@embl.de>
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Description-Content-Type: text/markdown

# LIANA+: an all-in-one cell-cell communication framework <img src="https://raw.githubusercontent.com/saezlab/liana-py/dev/docs/source/_static/logo.png?raw=true" align="right" height="125">

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LIANA+ is a scalable framework that adapts and extends existing methods and knowledge to study cell-cell communication in single-cell, spatially-resolved, and multi-modal omics data. It is part of the [scverse ecosystem](https://github.com/scverse), and relies on [AnnData](https://github.com/scverse/anndata) & [MuData](https://github.com/scverse/mudata) objects as input.

<img src="https://raw.githubusercontent.com/saezlab/liana-py/main/docs/_static/abstract.png" width="700" align="center">

## Contributions

We welcome suggestions, ideas, and contributions! Please do not hesitate to contact us, open issues, and check the [contributions guide](https://liana-py.readthedocs.io/en/latest/contributing.html).

## Vignettes
A set of extensive vignettes can be found in the [LIANA+ documentation](https://liana-py.readthedocs.io/en/latest/).

## Decision Tree
### 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)

#### Infer Metabolite-mediated CCC from transcriptomics?
- [Non-spatial Data](https://liana-py.readthedocs.io/en/latest/notebooks/sc_multi.html#Metabolite-mediated-CCC-from-Transcriptomics-Data)

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

## Cite LIANA+:

Dimitrov D., Schäfer P.S.L, Farr E., Rodriguez Mier P., Lobentanzer S., Badia-i-Mompel P., Dugourd A., Tanevski J., Ramirez Flores R.O. and Saez-Rodriguez J. LIANA+ provides an all-in-one framework for cell–cell communication inference. Nat Cell Biol (2024). https://doi.org/10.1038/s41556-024-01469-w

Dimitrov, D., Türei, D., Garrido-Rodriguez M., Burmedi P.L., Nagai, J.S., Boys, C., Flores, R.O.R., Kim, H., Szalai, B., Costa, I.G., Valdeolivas, A., Dugourd, A. and Saez-Rodriguez, J. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. Nat Commun 13, 3224 (2022). https://doi.org/10.1038/s41467-022-30755-0

Please also consider citing any of the methods and/or resources that were particularly relevant for your research!

[uv]: https://github.com/astral-sh/uv
[scverse discourse]: https://discourse.scverse.org/
[issue tracker]: https://github.com/saezlab/liana-py/issues
[tests]: https://github.com/dbdimitrov/liana-py/actions/workflows/test.yaml
[documentation]: https://liana-py.readthedocs.io
[changelog]: https://liana-py.readthedocs.io/en/latest/release_notes.html
[api documentation]: https://liana-py.readthedocs.io/en/latest/api.html
[pypi]: https://pypi.org/project/liana
