GeneCover: A Combinatorial Approach for Label-free Marker Gene Selection

Abstract

The selection of marker gene panels is critical for capturing the cellular and spatial heterogeneity in the expanding atlases of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics data. Most current approaches to marker gene selection operate in a label-based framework, which is inherently limited by its dependency on predefined cell type labels or clustering results. In contrast, existing label-free methods often struggle to identify genes that characterize rare cell types or subtle spatial patterns, and they frequently fail to scale efficiently with large datasets. Here, we introduce geneCover, a label-free combinatorial method that selects an optimal panel of minimally redundant marker genes based on gene-gene correlations. Our method demonstrates excellent scalability to large datasets and identifies marker gene panels that capture distinct correlation structures across the transcriptome. This allows geneCover to distinguish cell states in various tissues of living organisms effectively, including those associated with rare or otherwise difficult-to-identify cell types. We evaluate the performance of geneCover across various scRNA-seq and spatial transcriptomics datasets, comparing it to other unsupervised algorithms to highlight its utility and potential in diverse biological contexts.