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stochprofML: Stochastic profiling using maximum likelihood estimation in R.

BMC Bioinformatics 22:123 (2021)
Publ. Version/Full Text Research data DOI
Open Access Gold
Creative Commons Lizenzvertrag
Background: 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. Results: 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’s performance in simulation studies and present further application opportunities. Conclusion: Stochastic profiling outweighs the necessary demixing of mixed samples with a saving in experimental cost and effort and less measurement error. It offers possibilities for parameterizing heterogeneity, estimating underlying pool compositions and detecting differences between cell populations between samples.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Cell-to-cell Heterogeneity ; Deconvolution ; Gene Expression ; Maximum Likelihood Estimation ; Mixture Models ; R ; Stochastic Profiling ; Stochprofml
ISSN (print) / ISBN 1471-2105
e-ISSN 1471-2105
Quellenangaben Volume: 22, Issue: 1, Pages: , Article Number: 123 Supplement: ,
Publisher BioMed Central
Publishing Place Campus, 4 Crinan St, London N1 9xw, England
Reviewing status Peer reviewed
Grants Foundation for the National Institutes of Health
Helmholtz Initiating and Networking Funds

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