signatureSearch is an R/Bioconductor package that integrates a suite of existing 
and novel algorithms into an analysis environment for gene expression signature 
(GES) searching combined with functional enrichment analysis (FEA) and 
visualization methods to facilitate the interpretation of the search results. In 
a typical GES search (GESS), a query GES is searched against a database of GESs 
obtained from large numbers of measurements, such as different genetic 
backgrounds, disease states and drug perturbations. Database matches sharing 
correlated signatures with the query indicate related cellular responses 
frequently governed by connected mechanisms, such as drugs mimicking the 
expression responses of a disease. To identify which processes are predominantly 
modulated in the GESS results, we developed specialized FEA methods combined 
with drug-target network visualization tools. The provided analysis tools are 
useful for studying the effects of genetic, chemical and environmental 
perturbations on biological systems, as well as searching single cell GES 
databases to identify novel network connections or cell types. The 
signatureSearch software is unique in that it provides access to an integrated 
environment for GESS/FEA routines that includes several novel search and 
enrichment methods, efficient data structures, and access to pre-built GES 
databases, and allowing users to work with custom databases.