SAIGE-QTL is an R package developed with Rcpp for scalable and accurate expression quantitative trait locus mapping for single-cell studies

The method

• Model repeat and complex data structure, due to multiple cells per individual and relatedness between individuals
• Model discrete read counts
• Fast and scalable for large data, test 20k genes, 200 cell types, millions of cells, millions of variants
• Test rare variations. Single-variant test is underpowered

Please see https://weizhou0.github.io/SAIGE-QTL-doc/ for how to run SAIGE-QTL.