Author:
Raredon Micha Sam Brickman,Yang Junchen,Garritano James,Wang Meng,Kushnir Dan,Schupp Jonas Christian,Adams Taylor S.,Greaney Allison M.,Leiby Katherine L.,Kaminski Naftali,Kluger Yuval,Levchenko Andre,Niklason Laura E.
Abstract
AbstractSingle-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.
Funder
National Institutes of Health
U.S. Department of Defense
Publisher
Springer Science and Business Media LLC
Cited by
35 articles.
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