  We introduce PolyLinkR, an R package for gene set enrichment analysis that
implements a novel null-model that accounts for linkage disequilibrium between
genes belonging to the same gene set - a potential cause of false positives
that is often not controlled for in similar tools. Our benchmarks show that
PolyLinkR has improved performance compared to two similar tools, achieving
comparable power to detect enriched gene sets while producing less than one
falsely detected gene set on average, even at high genetic clustering levels
and nominal false discovery rates of 20%.
