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

IF 17.3 1区 生物学 Q1 CELL BIOLOGY Nature Cell Biology Pub Date : 2024-09-02 DOI:10.1038/s41556-024-01469-w
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
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Abstract

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-py with extensive vignettes ( https://liana-py.readthedocs.io/ ) and provides an all-in-one solution to intercellular communication inference. Dimitrov et al. present LIANA+, a framework that unifies and extends approaches to study inter- and intracellular signalling from diverse mediators, captured from single-cell, spatially resolved and multi-omics data.

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LIANA+ 为细胞间通信推断提供了一体化框架
随着单细胞和空间分辨转录组学的日益普及,人们开发出了许多推断细胞-细胞通讯的方法,但每种方法都只能捕捉到细胞间信号传导复杂图景的一部分。在这里,我们介绍 LIANA+,这是一个围绕丰富知识库建立的可扩展框架,用于从单细胞和空间分辨数据集的单条件和多条件数据中解码细胞间和细胞内协调的信号事件。通过扩展和统一既有方法,LIANA+ 提供了一套全面的协同组件,用于研究通过不同分子介质(包括在多组学数据中测量到的分子介质)进行的细胞-细胞通讯。LIANA+可通过 https://github.com/saezlab/liana-py 访问,并提供丰富的小节 (https://liana-py.readthedocs.io/),是细胞间通讯推断的一体化解决方案。
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来源期刊
Nature Cell Biology
Nature Cell Biology 生物-细胞生物学
CiteScore
28.40
自引率
0.90%
发文量
219
审稿时长
3 months
期刊介绍: Nature Cell Biology, a prestigious journal, upholds a commitment to publishing papers of the highest quality across all areas of cell biology, with a particular focus on elucidating mechanisms underlying fundamental cell biological processes. The journal's broad scope encompasses various areas of interest, including but not limited to: -Autophagy -Cancer biology -Cell adhesion and migration -Cell cycle and growth -Cell death -Chromatin and epigenetics -Cytoskeletal dynamics -Developmental biology -DNA replication and repair -Mechanisms of human disease -Mechanobiology -Membrane traffic and dynamics -Metabolism -Nuclear organization and dynamics -Organelle biology -Proteolysis and quality control -RNA biology -Signal transduction -Stem cell biology
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