signatureSearch

"signatureSearch" is an R package designed for gene expression signature (GES) searching, functional enrichment analysis (FEA), and result visualization. It integrates various existing and novel algorithms to facilitate the interpretation of GES search results. A typical GES search compares a query GES against a database of GESs from diverse measurements (e.g., genetic backgrounds, disease states, drug perturbations). Database matches with correlated signatures indicate related cellular responses, revealing connected mechanisms. The package includes specialized FEA methods with drug-target network visualization tools to identify predominantly modulated processes in the search results. "signatureSearch" is versatile, suitable for studying the effects of genetic, chemical, and environmental perturbations on biological systems, and allows users to work with both pre-built and custom GES databases.