CellKb Immune: a manually curated database of mammalian immune marker gene sets optimized for rapid cell type identification

Abstract

Single-cell RNA-seq is widely used to study transcriptional patterns of genes in individual cells. In spite of current advances in technology, assigning cell types in single-cell datasets remains a bottleneck due to the lack of a comprehensive reference database and a fast search method in a single tool. CellKb Immune is a knowledgebase of manually collected, curated and annotated marker gene sets from cell types in the mammalian immune response. It finds matching cell types in literature given a list of genes using a novel rank-based algorithm optimized for rapid searching across marker gene lists of differing lengths. We evaluated the contents and search algorithm of CellKb Immune using a leave-one-out approach. We further used CellKb Immune to annotate previously defined marker gene sets from Immgen to confirm its accuracy and coverage. CellKb Immune provides an easy to use database with a fast and reliable method to find matching cell types and annotate cells in single-cell experiments in a single tool. It is available at https://www.cellkb.com/immune.