BPSC – Beta-Poisson model for single-cell RNA-seq data analyses

Single-cell RNA-sequencing technology allows detection of gene expression at the single-cell level. One typical feature of the data is a bimodality in the cellular distribution even for highly expressed genes, primarily caused by a proportion of non-expressing cells. The standard and the over-dispersed gamma-Poisson models that are commonly used in bulk-cell RNA-sequencing are not able to capture this property.

Researchers at the Karolinska Institutet have devloped a beta-Poisson mixture model that can capture the bimodality of the single-cell gene expression distribution. They further integrate the model into the generalized linear model framework in order to perform differential expression analyses. The whole analytical procedure is called BPSC. The results from several real single-cell RNA-seq datasets indicate that ~90% of the transcripts are well characterized by the beta-Poisson model; the model-fit from BPSC is better than the fit of the standard gamma-Poisson model in >80% of the transcripts. Moreover, in differential expression analyses of simulated and real datasets, BPSC performs well against edgeR, a conventional method widely used in bulk-cell RNA-sequencing data, and against scde and MAST, two recent methods specifically designed for single-cell RNA-seq data.


BP3 model versus GP model in AIC scores from MDA-MB-231 dataset. In more than 80% of the transcripts, the AIC of the BP model (AICBP) is less than the AIC of the GP model (AICGP)

Availability: An R package BPSC for model fitting and differential expression analyses of single-cell RNA-seq data is available under GPL-3 license at https://github.com/nghiavtr/BPSC

Contact: yudi.pawitan@ki.se and mattias.rantalainen@ki.se

Vu TN, Wills QF, Kalari KR, Niu N, Wang L, Rantalainen M, Pawitan Y. (2016) Beta-Poisson model for single-cell RNA-seq data analyses. Bioinformatics [Epub ahead of print]. [abstract]

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