Inference of Gene Co-expression Networks from Single-Cell RNA-Sequencing Data
gene co-expression network; gene regulatory network; single-cell RNA-seq; correlation coefficient; count data; directed network; pseudotime
Computational Methods for Single-Cell Data Analysis
Single-cell RNA-sequencing is a pioneering extension of bulk-base RNA-sequencing technology. The "guilt-by-association" heuristic has led to the use of gene co-expression networks to identify genes that are believed to be associated with a common cellular function. Many methods that were developed for bulk-based RNA-sequencing data can continue to be applied to single-cell data, and several of the most widely used methods are explored. Several methods for leveraging the novel time information contained in single-cell data when constructing gene co-expression networks, which allows for the incorporation of directed associations, are also discussed.