stochprofML: Stochastic Profiling Using Maximum Likelihood Estimation in R

04/19/2020

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by   Lisa Amrhein, et al.

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Tissues are often heterogeneous in their single-cell molecular expression, and this can govern the regulation of cell fate. For the understanding of development and disease, it is important to quantify heterogeneity in a given tissue. We introduce the R package stochprofML which is designed to parameterize heterogeneity from the cumulative expression of small random pools of cells. This method outweighs the demixing of mixed samples with a saving in cost and effort and less measurement error. The approach uses the maximum likelihood principle and was originally presented in Bajikar et al.(2014); its extension to varying pool sizes was used in Tirier et al. (2019). We evaluate the algorithm's performance in simulation studies and present further application opportunities.