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Vignettes Overview

Source: vignettes/hdWGCNA.Rmd
hdWGCNA.Rmd

hdWGCNA Tutorials

Welcome to the hdWGCNA documentation! This page provides an overview of all available tutorials organized by topic.

Getting Started

Introduction to hdWGCNA

Learn about the background, motivation, and key concepts behind hdWGCNA.

Quick Start Guide

Get up and running with hdWGCNA in under 10 minutes with a minimal working example.

Algorithm and Mathematical Framework

Detailed explanation of the algorithms and mathematical foundations underlying hdWGCNA, including metacell aggregation, soft power thresholding, and module detection.

Core Tutorials

hdWGCNA in Single-Cell Data

Comprehensive tutorial covering co-expression network analysis in scRNA-seq data.

hdWGCNA in Spatial Transcriptomics

Learn how to construct co-expression networks from spatial transcriptomics data.

Network Visualization

Various approaches for visualizing hdWGCNA co-expression networks.

Biological Context

Differential Module Eigengene (DME) Analysis

Compare module eigengenes between experimental groups to identify condition-specific modules.

Module Trait Correlation

Correlate continuous and categorical variables with module eigengenes.

Enrichment Analysis

Use Enrichr to identify biological functions of co-expression modules.

Cross-Dataset Analysis

Projecting Modules to New Datasets

Project co-expression modules from a reference to a query dataset.

Module Preservation

Assess the preservation and reproducibility of co-expression networks.

Cross-Species and Cross-Modality Analysis

Special cases for projection when species or data modality differ.

Advanced Topics

Transcription Factor Network Analysis

Infer TF regulatory networks using XGBoost-based modeling.

PPI Network Integration

Integrate co-expression networks with protein-protein interaction data.

Consensus Network Analysis

Combine multiple datasets for robust network construction.

Pseudobulk Analysis

Use hdWGCNA with pseudobulk expression profiles.

Pseudotime Dynamics

Study module dynamics along pseudotime trajectories.

Other Topics

Module Customization

Change default names and colors for hdWGCNA modules.

Alternative Metacell Algorithms

Use alternative metacell construction methods.

Using SCTransform Data

Work with SCTransform normalized data in hdWGCNA.

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