epiregulon.extra

epiregulon.extra extends the epiregulon framework by providing additional plotting, differential analysis, and graph functions for gene regulatory network analysis.

Key Features:

• Plotting Functions: Provides additional visualization capabilities beyond the base epiregulon package.
• Differential Analysis Functions: Enables comparative statistical analysis of transcription factor activity and regulatory networks.
• Graph Functions: Supports network graph construction and manipulation for gene regulatory networks.

Scientific Applications:

• Single-Cell TF Activity Inference: Supports downstream analysis of transcription factor activity inferred from single-cell gene regulatory networks constructed from integrated scATAC-seq and scRNA-seq data.
• Gene Regulatory Network Visualization: Facilitates graphical representation of regulons and their regulatory hierarchies.
• Differential Regulatory Analysis: Enables comparison of gene regulatory networks across different cellular states or conditions.

Methodology:

The package serves as a companion to epiregulon, which constructs regulons by integrating scATAC-seq and scRNA-seq data with public bulk TF ChIP-seq data, establishing links between regulatory elements and target genes through correlation of chromatin accessibility and gene expression.