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bioRxiv · 10.1101/2020.12.01.389890

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

Patil, A.
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Abstract

Using single-cell RNA sequencing, it is now possible to get the detailed gene expression pattern in each cell for millions of cells in a single experiment under varying conditions. Annotating cells by assigning a type or state to them is important for correct interpretation of results. 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 an accurate search method in a single tool. CellKb Immune is a knowledgebase of manually collected, curated and annotated marker gene sets representing cell types in the immune response in mouse. It allows users to find matching cell types in literature given a list of genes. We evaluated the contents and search methodology of CellKb Immune using a leave-one-out approach. We further used CellKb Immune to annotate previously defined marker gene sets from a bulk RNA-seq dataset to confirm its accuracy and coverage. CellKb Immune provides an easy-to-use online tool with a reliable method to find matching cell types and annotate cells in single-cell experiments. It is available at https://www.cellkb.com/immune.

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Patil, A.. 2020-12-02. CellKb Immune: a manually curated database of mammalian immune marker gene sets optimized for rapid cell type identification. https://doi.org/10.1101/2020.12.01.389890

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