# hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data

Article · Morabito S, Reese F, Rahimzadeh N, Miyoshi E, Swarup V

- Archive id: doi:10.1016/j.crmeth.2023.100498
- Published: 2023-06-12
- Venue: Cell reports methods
- DOI: https://doi.org/10.1016/j.crmeth.2023.100498
- PMID: 37426759
- PMCID: PMC10326379
- Citations: 795
- Source URL: https://doi.org/10.1016/j.crmeth.2023.100498
- PDF: https://europepmc.org/articles/PMC10326379/pdf
- Provenance: europepmc

## Abstract

Biological systems are immensely complex, organized into a multi-scale hierarchy of functional units based on tightly regulated interactions between distinct molecules, cells, organs, and organisms. While experimental methods enable transcriptome-wide measurements across millions of cells, popular bioinformatic tools do not support systems-level analysis. Here we present hdWGCNA, a comprehensive framework for analyzing co-expression networks in high-dimensional transcriptomics data such as single-cell and spatial RNA sequencing (RNA-seq). hdWGCNA provides functions for network inference, gene module identification, gene enrichment analysis, statistical tests, and data visualization. Beyond conventional single-cell RNA-seq, hdWGCNA is capable of performing isoform-level network analysis using long-read single-cell data. We showcase hdWGCNA using data from autism spectrum disorder and Alzheimer's disease brain samples, identifying disease-relevant co-expression network modules. hdWGCNA is directly compatible with Seurat, a widely used R package for single-cell and spatial transcriptomics analysis, and we demonstrate the scalability of hdWGCNA by analyzing a dataset containing nearly 1 million cells.

_Abstract reproduced under CC-BY (article license as recorded by Europe PMC; abstract reproduced unmodified apart from markup removal)._

Topics: [Single-Cell & Spatial Omics](https://space-kitty.com/topics/single-cell-spatial)

Cited in dossiers:
- [Single-Cell & Spatial Omics: State of the Field (October 2026)](https://space-kitty.com/dossiers/single-cell-spatial)

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