vizAPA

vizAPA visualizes alternative polyadenylation (APA) dynamics from bulk and single-cell datasets as an R package to support investigation of APA-mediated post-transcriptional gene regulation.

Key Features:

• Unified Data Structures: Implements a cohesive framework that integrates APA site data with genome annotations.
• Differential APA Usage Identification: Identifies genes exhibiting differential APA usage across biological samples or cell types.
• Four Visualization Modules: Provides four distinct visualization modules tailored to explore APA dynamics at both bulk and single-cell resolution.
• Pipeline Integration: Provides a plugin interface for incorporation into APA analysis pipelines.

Scientific Applications:

• Comparative Analysis: Compare APA usage across different biological samples or cell types to identify context-specific regulatory mechanisms.
• Single-Cell Resolution Studies: Analyze single-cell datasets to assess cell-level heterogeneity in APA dynamics.
• Integration with Existing Workflows: Extend routine APA analysis pipelines by incorporating visualization and differential-usage modules.

Methodology:

Implements unified APA and genome-annotation data structures, differential APA usage identification, and four visualization modules within an R package provided for pipeline integration.