Imputation Methods for scRNA Sequencing Data

Author:

Wang Mengyuan,Gan Jiatao,Han Changfeng,Guo Yanbing,Chen Kaihao,Shi Ya-zhou,Zhang Ben-gongORCID

Abstract

More and more researchers use single-cell RNA sequencing (scRNA-seq) technology to characterize the transcriptional map at the single-cell level. They use it to study the heterogeneity of complex tissues, transcriptome dynamics, and the diversity of unknown organisms. However, there are generally lots of technical and biological noises in the scRNA-seq data since the randomness of gene expression patterns. These data are often characterized by high-dimension, sparsity, large number of “dropout” values, and affected by batch effects. A large number of “dropout” values in scRNA-seq data seriously conceal the important relationship between genes and hinder the downstream analysis. Therefore, the imputation of dropout values of scRNA-seq data is particularly important. We classify, analyze and compare the current advanced scRNA-seq data imputation methods from different angles. Through the comparison and analysis of the principle, advantages and disadvantages of the algorithm, it can provide suggestions for the selection of imputation methods for specific problems and diverse data, and have basic research significance for the downstream function analysis of data.

Funder

National Natural Science Foundation of China

Publisher

MDPI AG

Subject

Fluid Flow and Transfer Processes,Computer Science Applications,Process Chemistry and Technology,General Engineering,Instrumentation,General Materials Science

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