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LIANA+: an all-in-one cell-cell communication framework

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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.

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

No

Is your data Multi-modal?

Infer Metabolite-mediated CCC from transcriptomics?

Non-spatial Data

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!