PathVisioRPC

PathVisioRPC provides programmatic access to PathVisio for creating, editing, visualizing, and statistically analyzing biological pathways from external scripting languages.

Key Features:

• Integration with scripting languages: Enables remote control of PathVisio functionality from external scripting languages via RPC.
• Pathway creation and editing: Supports creation and modification of pathway diagrams within PathVisio programmatically.
• Data visualization on pathways: Maps experimental data onto pathway elements for pathway-level visualization.
• Statistical pathway analysis: Performs statistical analyses of pathways using PathVisio's analysis capabilities invoked remotely.
• Export to image formats: Exports pathway visualizations to various image formats.
• R integration (RPathVisio): Includes the RPathVisio module to enable integration with the R environment and R-based scripts.
• Automation capabilities: Automates repetitive PathVisio tasks to enable scripted batch analyses.
• Support for pathway sources: Supports use of existing pathways from databases such as WikiPathways and custom pathways created via RPC.

Scientific Applications:

• Functional analysis of differentially expressed genes or proteins: Enables pathway-level interpretation and visualization of differentially expressed genes or proteins.
• Integration with R-based workflows and public datasets: Integrates with R data-processing scripts and packages and can be applied to NCBI GEO gene expression datasets (for example, datasets involving tumor-bearing mice treated with cyclophosphamide).

Methodology:

PathVisioRPC leverages XML-RPC to bridge PathVisio's pathway analysis capabilities with external scripting languages.