Matrix eQTL 2.1.0
Matrix eQTL can model and test for association using both linear regression and ANOVA models. The models can include covariates to account for such factors as population structure, gender, and clinical variables. It also supports testing of heteroscedastic models and models with correlated errors. In our experiment on large datasets Matrix eQTL was thousands of times faster than the existing popular software for QTL/eQTL analysis.
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Matrix eQTL: ultra fast eQTL analysis via large matrix operations.
Bioinformatics. 2012 May 15;28(10):1353-8. doi: 10.1093/bioinformatics/bts163. Epub 2012 Apr 6.