RedeR

RedeR provides visualization and analysis of modular and hierarchical molecular networks for systems biology using an R/Bioconductor package in conjunction with a Java core engine.

Key Features:

• Modular Network Representation: Represents modular structures within molecular networks to support analysis of network modules.
• Hierarchical Organization: Handles hierarchical organization in gene co-expression networks to enable exploration of nested and multi-level associations.
• Nested Structures Analysis: Supports analysis of nested structures within time-course gene expression subnetworks to investigate dynamic regulatory patterns.
• Visualization Engine: Integrates a Java core engine with an R/Bioconductor package to generate graphical representations of complex network structures.
• Multi-level Network Handling: Addresses multiple network levels and hierarchies within complex biological systems.

Scientific Applications:

• Gene co-expression network analysis: Analyze hierarchical and modular organization of gene co-expression networks.
• Time-course gene expression subnetworks: Investigate nested temporal structures in time-course gene expression subnetworks.
• Systems biology multi-level network studies: Explore relationships across multiple network levels in complex biological systems.

Methodology:

RedeR combines an R/Bioconductor package with a Java core engine to perform visualization and manipulation of hierarchical and modular network structures.