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Bioinformatician’s main tool for discovery has often been differential expression analysis. But between Enrich, Prerank, GSEA, ssGSEA, which tool should you use? here is the quick reminder X-plainer:

Enrichr is when you just have a list of genes (can be small):

GENEA, GENEB, GENEC

Prerank is when you have values that you can rank your list of genes from:

Gene Value
GENEA 12
GENEB 8
GENEC 4

GSEA works best when you have a list of genes, with values associated with them across multiple conditions (and replicates):

Gene C1 C2 C3 D1 D2 D3
GENEA 12 7 3 1 1 0
GENEB 8 0 6 8 1 1
GENEC 4 4 3 2 3 4

ssGSEA is when you have many values associated with them but not 2 specific condition and want to compare 1 vs the rest

Gene A B C D E F
GENEA 12 7 3 1 1 0
GENEB 8 0 6 8 1 1
GENEC 4 4 3 2 3 4

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