Computation and visualization of cell–cell signaling topologies in single-cell systems data using Connectome
Abstract
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Mar 09, 2022
- Source ID
- 10.1038/s41598-022-07959-x
Entities
People
- Allison M. Greaney
- Andre Levchenko
- Dan Kushnir
- James Garritano
- Jonas Christian Schupp
- Junchen Yang
- Katherine L. Leiby
- Laura E Niklason
- Meng Wang
- Micha Sam Brickman Raredon
- Naftali Kaminski
- Taylor S. Adams
- Yuval Kluger
Organizations
- National Institutes of Health
- United States Department of Defense