VIPER: variability-preserving imputation for accurate gene expression recovery in single-cell RNA sequencing studies

• Published in: Genome Biology Vol. 19; no. 1; p. 196
• Main Authors: Chen, Mengjie, Zhou, Xiang
• Format: Journal Article
• Language: English
• Published: England BioMed Central 12.11.2018; BMC
• Subjects: Bioinformatics; Data processing; DNA methylation; Gene expression; Gene Expression Profiling - methods; genome; Genomes; Genomics; Method; Methods; Parameter estimation; Regression Analysis; Ribonucleic acid; RNA; Sequence Analysis, RNA; Single-Cell Analysis; Stem cells; transcriptome

We develop a method, VIPER, to impute the zero values in single-cell RNA sequencing studies to facilitate accurate transcriptome quantification at the single-cell level. VIPER is based on nonnegative sparse regression models and is capable of progressively inferring a sparse set of local neighborhoo...