README.md

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

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

• 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
  • Unsupervised: Multi-view learning

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
  • No: Steady-state Ligand-Receptor inference

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?

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!