SPAROscore - A package to compute gene signature scores from transcriptomics data

SPAROscore is a gene signature scoring method designed to be robust across diverse gene expression datasets. SPAROscore adapts to varying levels of sparsity, allowing signature scores to be efficiently computed across bulk, single-cell, and spatial transcriptomic datasets. The resulting scores quantify the relative expression of a gene signature compared with the background expression of each sample/cell/domain, making the scores straightforward to interpret biologically. Internally, SPAROscore ranks genes within each column and computes the Spearman footrule distance between the observed ranks of the signature genes and a background gene expression rank estimated from the geometric mean expression of the sample, cell, or spatial domain.