Articles • hdWGCNA

Introduction to hdWGCNA: A comprehensive introduction to hdWGCNA: background, motivation, and key concepts.
Quick Start Guide: Get started with hdWGCNA in 10 minutes - a minimal example of co-expression network analysis.
Algorithm and Mathematical Framework: Comprehensive overview of the algorithms and mathematical foundations underlying hdWGCNA.

hdWGCNA in single-cell data: Tutorial for applying the core functions of hdWGCNA in single-cell data.
hdWGCNA in spatial transcriptomics: Tutorial for applying the core functions of hdWGCNA in spatial transcriptomics data.
Isoform co-expression network analysis with PacBio MAS-Seq: Full Seurat clustering and hdWGCNA analysis tutorial of PacBio MAS-Seq PBMC dataset.
Network Visualization: Tutorial for visualizing the hdWGCNA networks using igraph.

Differential module eigengene (DME) analysis: Tutorial for performing differential module eigengene analysis.
Module Trait Correlation: Tutorial for identifying relationships between hdWGCNA modules with biological and technical variables.
Enrichment analysis: Tutorial for performing enrichment analysis with hdWGCNA.

Projecting modules to new datasets: Tutorial for applying the core functions of hdWGCNA.
Module preservation and reproducibility: Tutorial for performing module preservation tests in hdWGCNA.
Cross-species and cross-modality analysis: Projecting hdWGCNA co-expression modules across species and -omics modalities.

Transcription factor regulatory network analysis: Tutorial for using hdWGCNA for transcription factor regulatory network analysis.
Integrating co-expression and protein-protein interaction networks: Integrating co-expression and protein-protein interaction networks
Consensus network analysis: Tutorial for performing consensus co-expression network analysis.
hdWGCNA with pseudobulk data: Tutorial for running hdWGCNA with pseudobulk data rather than metacells/metaspots .
Co-expression module dynamics with pseudotime: Co-expression module dynamics with pseudotime.
Motif Analysis: Tutorial for identifying transcription factor binding motifs that are related to hdWGCNA modules.

Module customization: Tutorial for customizing module colors and module names in hdWGCNA.
Alternative metacell algorithms: Tutorial for performing co-expression network analysis using alternative metacell aggregation algorithms.
Using SCTransform normalized data: Tutorial demonstrating hdWGCNA with SCTransform normalized data.