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I have yeast growth data in various experimental conditions that are classified by the strain type. Can I use the GSEA tool from the Broad Institute to test for enrichment of specific groups of strains within the total population (i.e. gene sets)? If not, would something like a hypergeomtric test be useful for this kind of analysis?

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Yes, if you have a ranked list, you can use GSEA to calculate the enrichment of the strains along the ranked list.

Note that hypergeometric test is for count data, so you would test if there are more strains of one type that fit on certain conditions.

I would recommend this article comparing different enrichment methods to understand well what they do.

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