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LIANA+ provides an all-in-one framework for cell-cell communication inference

The growing availability of single-cell and spatially resolved transcriptomics has led to the development of many approaches to infer cell-cell communication, each capturing only a partial view of the complex landscape of intercellular signalling. Here we present LIANA+, a scalable framework built a...

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Hauptverfasser: Dimitrov, Daniel (VerfasserIn) , Schäfer, Philipp (VerfasserIn) , Farr, Elias (VerfasserIn) , Rodriguez Mier, Pablo (VerfasserIn) , Lobentanzer, Sebastian (VerfasserIn) , Badia-i-Mompel, Pau (VerfasserIn) , Dugourd, Aurélien (VerfasserIn) , Tanevski, Jovan (VerfasserIn) , Ramirez Flores, Ricardo O. (VerfasserIn) , Sáez Rodríguez, Julio (VerfasserIn)
Dokumenttyp: Article (Journal)
Sprache:Englisch
Veröffentlicht: 02 September 2024
In: Nature cell biology
Year: 2024, Jahrgang: 26, Heft: 9, Pages: 1613-1622
ISSN:1476-4679
DOI:10.1038/s41556-024-01469-w
Online-Zugang:Verlag, kostenfrei, Volltext: https://doi.org/10.1038/s41556-024-01469-w
Verlag, kostenfrei, Volltext: https://www.nature.com/articles/s41556-024-01469-w
Volltext
Verfasserangaben: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
Beschreibung
Zusammenfassung:The growing availability of single-cell and spatially resolved transcriptomics has led to the development of many approaches to infer cell-cell communication, each capturing only a partial view of the complex landscape of intercellular signalling. Here we present LIANA+, a scalable framework built around a rich knowledge base to decode coordinated inter- and intracellular signalling events from single- and multi-condition datasets in both single-cell and spatially resolved data. By extending and unifying established methodologies, LIANA+ provides a comprehensive set of synergistic components to study cell-cell communication via diverse molecular mediators, including those measured in multi-omics data. LIANA+ is accessible at https://github.com/saezlab/liana-pywith extensive vignettes (https://liana-py.readthedocs.io/) and provides an all-in-one solution to intercellular communication inference.
Beschreibung:Gesehen am 07.10.2024
Beschreibung:Online Resource
ISSN:1476-4679
DOI:10.1038/s41556-024-01469-w

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