SBGNview

SBGNview provides pathway analysis and visualization using the Systems Biology Graphical Notation (SBGN) standard for genomics and omics research.

Key Features:

• R package: Implemented as an R package for integration in R-based analysis workflows.
• SBGN standard support: Uses the Systems Biology Graphical Notation (SBGN) standard for pathway representation.
• Extensive pathway coverage: Supports over 5,200 reference pathways covering more than 3,000 species.
• Standardized data formats: Reads and writes SBGN format files for input and output.
• High-quality graphics: Generates high-quality graphical representations of pathways that are computationally efficient.
• Flexible workflow: Provides a flexible, open-ended workflow for custom analyses.
• Data manipulation infrastructure: Includes functions for manipulating and processing SBGN data.
• Pathview integration: Extends capabilities of Pathview by leveraging SBGN for pathway-based analyses.

Scientific Applications:

• Genomics and omics pathway analysis: Enables pathway-based analysis of genomics and other omics datasets.
• Visualization of cellular interactions: Facilitates visualization and interpretation of complex interactions within cellular systems.
• Comparative pathway studies: Supports comparative pathway analyses across multiple databases and species.

Methodology:

Leverages the Systems Biology Graphical Notation (SBGN) standard and SBGN file format for pathway representation, extends Pathview functionality, and provides computational functions to manipulate and process SBGN data.