“Simple Tidy GeneCoEx”: A gene co‐expression analysis workflow powered by tidyverse and graph‐based clustering in R

2023/04/16 by Chenxin Li, Natalie C. Deans, C. Robin Buell · 1 voice · 1 citation
Biochemistry, Genetics and Molecular Biology · #Bioinformatics and Genomic Networks #Gene Regulatory Network Analysis #Gene expression and cancer classification

paper · pdf · doi:10.1002/tpg2.20323

openalex publication_date 2023/04/16 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

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.

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Discussions

• “Simple Tidy GeneCoEx”: A gene co-expression analysis workflow powered by tidyverse and graph-based clustering in R doi.org/10.1002/tpg2... by @chenxinli2.bsky.social [bsky, 1 points, 0 comments]

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