"Simple Tidy GeneCoEx": A gene co-expression analysis workflow powered by tidyverse and graph-based clustering in R

Plant Genome. 2023 Jun;16(2):e20323. doi: 10.1002/tpg2.20323. Epub 2023 Apr 16.

Abstract

Gene co-expression analysis is an effective method to detect groups (or modules) of co-expressed genes that display similar expression patterns, which may function in the same biological processes. Here, we present "Simple Tidy GeneCoEx", a gene co-expression analysis workflow written in the R programming language. The workflow is highly customizable across multiple stages of the pipeline including gene selection, edge selection, clustering resolution, and data visualization. Powered by the tidyverse package ecosystem and network analysis functions provided by the igraph package, the workflow detects gene co-expression modules whose members are highly interconnected. Step-by-step instructions with two use case examples as well as source code are available at https://github.com/cxli233/SimpleTidy_GeneCoEx.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Cluster Analysis
  • Gene Expression Profiling
  • Gene Expression*
  • Gene Regulatory Networks
  • Workflow

Associated data

  • Dryad/10.5061/dryad.6q573n5w2