scCoExpress: A Sparsity-Aware R Package for Gene Co-Expression Analysis in Single-Cell Datasets

<ns5:p>Abstract* With the advent of single-cell and spatial transcriptomics, many research groups are interested in identifying genes which are disproportionately expressed in the same cells at the same time. However, due to the sparsity of single cell data at the level of individual cells, this can be challenging. Here, we present scCoExpress: a Seurat-compatible R package that queries the co-expression intensity of gene pairs by scaling co-expression against a background distribution of similarly abundant gene-gene comparisons.</ns5:p>