EasyCellType: marker-based cell-type annotation by automatically querying multiple databases

MOTIVATION: Cell label annotation is a challenging step in the analysis of single-cell RNA sequencing (scRNA-seq) data, especially for tissue types that are less commonly studied. The accumulation of scRNA-seq studies and biological knowledge leads to several well-maintained cell marker databases. Manually examining the cell marker lists against these databases can be difficult due to the large amount of available information. Additionally, simply overlapping the two lists without considering gene ranking might lead to unreliable results. Thus, an automated method with careful statistical testing is needed to facilitate the usage of these databases. RESULTS: We develop a user-friendly computational tool, EasyCellType, which automatically checks an input marker list obtained by differential expression analysis against the databases and provides annotation recommendations in graphical outcomes. The package provides two statistical tests, gene set enrichment analysis and a modified version of Fisher’s exact test, as well as customized database and tissue type choices. We also provide an interactive shiny application to annotate cells in a user-friendly graphical user interface. The simulation study and real-data applications demonstrate favorable results by the proposed method. AVAILABILITY AND IMPLEMENTATION: https://biostatistics.mdanderson.org/shinyapps/EasyCellType/; https://bioconductor.org/packages/devel/bioc/html/EasyCellType.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.