INDEED

The software tool "INDEED" addresses the need for advanced computational methods to analyze omics data to identify disease-associated biomolecules. While traditional differential expression analysis methods focus on mean and variance, network-based approaches consider interactions between biomolecules. However, existing methods often generate complex networks with indirect associations. INDEED, an R package introduces a novel approach by constructing a sparse network based on partial correlation. It identifies biomolecules with significant changes at individual expression and pairwise interaction levels. INDEED's framework is adaptable for future expansion to integrate networks from multi-omic studies, allowing the selection of reliable disease-associated biomolecules or biomarkers.