Computation and visualization of cell-cell signaling topologies in single-cell systems data using Connectome.
Computation and visualization of cell-cell signaling topologies in single-cell systems data using Connectome.
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DOI：
10.1038/s41598-022-07959-x
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发表时间：
2022-03-09
影响因子：
4.6
通讯作者：
Niklason LE
中科院分区：
文献类型：
--
作者：
Raredon MSB;Yang J;Garritano J;Wang M;Kushnir D;Schupp JC;Adams TS;Greaney AM;Leiby KL;Kaminski N;Kluger Y;Levchenko A;Niklason LE
Single-cell RNA-sequencing data has revolutionized our ability to understand of the patterns of cell–cell and ligand–receptor connectivity that influence the function of tissues and organs. However, the quantification and visualization of these patterns in a way that informs tissue biology are major computational and epistemological challenges. Here, we present Connectome, a software package for R which facilitates rapid calculation and interactive exploration of cell–cell signaling network topologies contained in single-cell RNA-sequencing data. Connectome can be used with any reference set of known ligand–receptor mechanisms. It has built-in functionality to facilitate differential and comparative connectomics, in which signaling networks are compared between tissue systems. Connectome focuses on computational and graphical tools designed to analyze and explore cell–cell connectivity patterns across disparate single-cell datasets and reveal biologic insight. We present approaches to quantify focused network topologies and discuss some of the biologic theory leading to their design.
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影响因子：
16.6
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Ramilowski JA;Goldberg T;Harshbarger J;Kloppmann E;Lizio M;Satagopam VP;Itoh M;Kawaji H;Carninci P;Rost B;Forrest AR
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Forrest AR
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4.6
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Ridolfi, Luca
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Saeys, Yvan
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64.8
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Teichmann SA
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4
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Manning EP;Ramachandra AB;Schupp JC;Cavinato C;Raredon MSB;Bärnthaler T;Cosme C Jr;Singh I;Tellides G;Kaminski N;Humphrey JD
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Humphrey JD