Hypergeometric test are useful for enrichment analysis. For example, having a gene list in hand, people might want to tell which functions (GO terms) are enriched among these genes. Hypergeometric test (or its equivalent: one-tailed Fisher's exact test) will give you statistical confidence in \(p\)-values.
R software provids function phyper and fisher.test for Hypergeometric and Fisher's exact test accordingly. However, it is tricky to get it right. I spent some time to make it clear.