PRIME – a probabilistic imputation method to reduce dropout effects in single cell RNA sequencing

Single-cell RNA sequencing technology provides a novel means to analyze the transcriptomic profiles of individual cells. The technique is vulnerable, however, to a type of noise called dropout effects, which lead to zero-inflated distributions in the transcriptome profile and reduce the reliability of the results. Single-cell RNA sequencing data therefore need to be carefully processed before in-depth analysis.

Researchers from Incheon National University and Texas Children’s Hospital have developed a novel imputation method that reduces dropout effects in single-cell sequencing. They construct a cell correspondence network and adjust gene expression estimates based on transcriptome profiles for the local subnetwork of cells of the same type. The researchers comprehensively evaluated this method, called PRIME (PRobabilistic IMputation to reduce dropout effects in Expression profiles of single cell sequencing), on synthetic and eight real single cell sequencing datasets and verified that it improves the quality of visualization and accuracy of clustering analysis and can discover gene expression patterns hidden by noise.

Overview of PRIME Alt text

Availability: The source code for the proposed method is freely available at

Jeong H, Liu Z. (2020) PRIME: a probabilistic imputation method to reduce dropout effects in single cell RNA sequencing. Bioinformatics [Epub ahead of print]. [abstract]

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