Cyrface

Cyrface integrates R with Cytoscape using Java–R libraries (Rserve, RCaller) to execute R/Bioconductor analyses and link statistical results to network visualization for biological research.

Key Features:

• Plug-in Architecture: Operates as a Cytoscape plug-in and as a library that allows other Cytoscape plug-ins to connect to R.
• Java–R Integration: Utilizes Java–R libraries such as Rserve and RCaller to enable communication and execution of R commands from within Cytoscape.
• Bioconductor Integration: Allows execution of functions and packages developed in R, including Bioconductor packages, directly from Cytoscape.
• Network analysis linkage: Links R's analytical capabilities with Cytoscape's network visualization to enable combined analysis and visualization of biological networks.

Scientific Applications:

• CellNOptR integration: Enables use of the Bioconductor package CellNOptR within Cytoscape for optimizing cellular network models.
• DrugVsDisease integration: Enables use of the Bioconductor package DrugVsDisease within Cytoscape for exploring drug–disease relationships.
• Systems biology, genomics, and pharmacology: Supports workflows that combine statistical analysis and network visualization for research in systems biology, genomics, and pharmacology.

Methodology:

Leverages Java–R libraries such as Rserve and RCaller to establish an interface between R and Cytoscape and to execute R commands within the Cytoscape environment.