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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, and relies on AnnData & MuData objects as input.
<img src="https://raw.githubusercontent.com/saezlab/liana-py/main/docs/source/_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.
Vignettes
A set of extensive vignettes can be found in the LIANA+ documentation.
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
- No: Check the Global Bivariate Metrics
- Q: Are you interested in identifying the subregions of interactions (i.e., local interactions)?
- Unsupervised: Multi-view learning
- Bivariate:
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
- No: Unsupervised Cross-conditional LR inference with MOFA+ or Tensor-cell2cell
- Q: Are you interested in a specific contrast?
- No: Steady-state Ligand-Receptor inference
- Yes:
Is your data Multi-modal?
- Spatial: Integrating Multi-Modal Spatially-Resolved Technologies
- Non-Spatial: Integrating Multi-Modal Single-Cell Technologies
Infer Metabolite-mediated CCC from transcriptomics?
API
For further information please check LIANA's API documentation.
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!