scCATCH: automatic annotation on cell-types of clusters from single-cell RNA-seq data

Summary Recent advancements in single-cell RNA sequencing (scRNA-seq) have facilitated the classification of thousands of cells through transcriptome profiling, wherein accurate cell-type identification is critical for mechanistic studies. In most of current analysis protocols, cell type-based cluster annotation is manually performed and heavily relies on prior knowledge, resulting in poor replicability of cell type annotation. This study aimed to introduce a single-cell Cluster-based automatic Annotation Toolkit for Cellular Heterogeneity (scCATCH, https://github.com/ZJUFanLab/scCATCH). Using three benchmark datasets, the feasibility of evidence-based scoring and tissue-specific cellular annotation strategies were demonstrated by high concordance among cell types and scCATCH outperformed than Seurat, a popular method for marker genes identification, and cell-based annotation methods. Furthermore, scCATCH accurately annotated 67–100% (average, 83%) of clusters in six published scRNA-seq datasets originated from various tissues. The present results show scCATCH accurately revealed cell identities with high reproducibility, thus potentially providing insights into mechanisms underlying disease pathogenesis and progression.