kruX: Matrix-based non-parametric eQTL discovery
Jianlong Qi, Hassan Foroughi Asl, Johan Bjorkegren, Tom Michoel
(Submitted on 12 Jul 2013)

The Kruskal-Wallis test is a popular non-parametric statistical test for identifying expression quantitative trait loci (eQTLs) from genome-wide data due to its robustness against variations in the underlying genetic model and expression trait distribution, but testing billions of marker-trait combinations one-by-one can become computationally prohibitive. We developed kruX, an algorithm implemented in Matlab, Python and R that uses matrix multiplications to simultaneously calculate the Kruskal-Wallis test statistic for several millions of marker-trait combinations at once. KruX is more than 3,000 times faster than computing associations one-by-one on a typical human dataset.