MIMOSA (Mixture Models for Single Cell Assays) fits a beta-binomial or Multinomial-Dirichlet model to count data from intracellular cytokine staining (ICS) flow cytometry data to assess whether individuals exhibit an antigen-specific response in pre-specified subsets of T-cells. The model is also useful for assessing antigen-specific response in other single-cell assays that generate count data of single-cells.