A preprint of our paper kruX: Matrix-based non-parametric eQTL discovery is available from the arXiv. This paper describes a software tool called kruX for performing millions of non-parametric ANOVA (Kruskal-Wallis) tests at once using matrix-multiplication methods. kruX is about 3 orders of magnitude faster than performing these tests one-by-one, which makes a difference if you want to do billions of them!
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