clustermole: blindly digging for cell types in scRNA-seq clusters

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See, children, the misguided Mole.
He lives down in a deep, dark hole;
Sweetness, and light, and good fresh air
Are things for which he does not care.
He has not even that makeshift
Of feeble minds - the social gift.
But say not that he has no soul,
Lest haply we misjudge the Mole;
Nay, if we measure him by men,
No doubt he sits in his dark den
Instructing others blind as he
Exactly how the world should be.

– Oliver Herford

A typical computational pipeline to process single-cell RNA sequencing (scRNA-seq) data involves clustering of cells. Assignment of cell type labels to those clusters is often a time-consuming process that involves manual inspection of the cluster marker genes complemented with a detailed literature search. This is especially challenging if you are not familiar with all the captured subpopulations or have unexpected contaminants. clustermole is an R package that provides a comprehensive meta collection of cell identity markers for thousands of human and mouse cell types sourced from a variety of databases as well as methods to query them.

Install clustermole (development version):

BiocManager::install("igordot/clustermole", update = FALSE)

Load clustermole:


Retrieve a table of all cell type markers:

clustermole_markers(genes, species)

Perform cell type overrepresentation analysis for a given set of genes:

clustermole_overlaps(expr_mat, species)

Perform cell type enrichment for a given full gene expression matrix:

clustermole_enrichment(expr_mat, species)