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eigenmt website  

eigenMT is a computationally efficient multiple testing correction method for cis-eQTL studies. Typically, modern cis-eQTL studies correct for multiple testing across thousands of variants for a single gene using permutations. This correction method, though accurate, requires a high computational cost on the order of days to weeks for large numbers of permutations and/or large sample sizes. Our method reduces this computational burden by orders of magnitude while maintaining high accuracy when compared to permutations. To accomplish this, our method attempts to estimate the number of effective tests performed for a given gene by directly accounting for the LD relationship among the tested variants.

Required Modules


  • eigenmt

System Variables

  • HPC_EIGENMT_DIR - installation directory


If you publish research that uses eigenmt you have to cite it as follows:

Davis, JR, Fresard, L, et al. eigenMT: efficient multiple hypothesis testing correction for eQTLs.