zingeR

The software tool 'zingeR' addresses the challenge of dropout-induced excess zero counts in single-cell RNA sequencing (scRNA-seq) data. These zero counts pose problems for differential expression (DE) analysis, leading to the development of specialized scRNA-seq DE tools. However, recent evaluations have shown no significant advantage of these tools over traditional bulk RNA-seq tools. 'zingeR' introduces a solution by presenting a zero-inflated negative binomial model that detects excess zero counts and generates observation weights. This enables the adaptation of bulk RNA-seq pipelines to accommodate zero-inflation, thereby enhancing the performance of scRNA-seq DE analysis.