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The first step consists in gathering all the input data in a comprehensive manner via the Eqmr-db program. But caution, each type of data must be formatted in a particular way (Category:File Format). It is possible to query the resulting databank with the Eqmr-dbget program.

Once this is done, the Eqmr-fdb program allows to summarize the phenotype data into a feature databank, for instance at the gene level if the initial data were given at the probe level. The results can be exported using the Eqmr-fexp program.

Then, the Eqmr-fcr program performs Bayesian linear regression for each feature with their SNPs in cis. The results can be exported using the Eqmr-fcrout program.

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