ibh

ibh calculates Interaction Based Homogeneity (IBH) to evaluate the fitness of gene lists within interaction networks for assessing clustering results and gene list coherence.

Key Features:

• Interaction Based Homogeneity (IBH) calculation: Computes the IBH metric to quantify how well a gene set aligns with an interaction network.
• BioGRID integration: Leverages BioGRID protein-protein and genetic interaction data as a default interaction resource.
• Custom interaction support: Accepts user-supplied interaction datasets in place of or alongside BioGRID.
• Gene list and clustering evaluation: Assesses the fitness and coherence of gene lists and clustering results within interaction networks.
• R/Bioconductor implementation: Provided as an R package within the Bioconductor ecosystem.

Scientific Applications:

• Clustering validation: Validates gene clustering results by measuring network coherence with the IBH metric.
• Gene list analysis: Evaluates functional coherence of gene lists relative to interaction networks and biological pathways.
• Network-based assessment: Uses BioGRID or custom interactions to contextualize gene sets within protein-protein and genetic interaction networks.
• Genomics and molecular biology research: Applies network coherence metrics to genomic and molecular datasets for downstream analysis.

Methodology:

Computes the Interaction Based Homogeneity (IBH) metric using interaction edges from BioGRID or user-supplied interaction datasets; implemented as an R package within Bioconductor.