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For the understanding of development and disease, it is important to quantify heterogeneity in a given tissue.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present the R package stochprofML which uses the maximum likelihood principle to parameterize heterogeneity from the cumulative expression of small random pools of cells. We evaluate the algorithm\u2019s performance in simulation studies and present further application opportunities.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Stochastic profiling outweighs the necessary demixing of mixed samples with a saving in experimental cost and effort and less measurement error. 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