Assignment of cell type labels to single-cell RNA sequencing (scRNA-seq) clusters is often a time-consuming process that involves manual inspection of the cluster marker genes complemented with a detailed literature search. This can be especially challenging when unexpected or poorly described populations are present. The clustermole R package provides methods to query cell identity markers from manually curated and computationally derived databases, including CellMarker, PanglaoDB, ScType, MSigDB, and xCell. Using several sources offers a broader view as the curation methods and selection criteria can differ. Comparing databases helps in discovering recurring candidates and markers that a single source may not cover.
To learn more about clustermole, check an overview of the features and an example workflow starting with a Seurat object.
Image credit: “A Child’s Primer Of Natural History” by Oliver Herford