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| Feature | Traditional Over-Representation Analysis (ORA) | sSNAPPY | | :--- | :--- | :--- | | | Counts of differentially expressed genes in a list | Propagates changes through pathway topologies (gene-gene interactions) | | Direction of Change | Typically cannot predict activation vs. suppression | Directly predicts the directional change of pathway activity | | Resolution | Works best at a group level (case vs. control) | Performs single-sample analysis , revealing heterogeneity within a group | | Statistical Approach | Hypergeometric or Fisher's exact tests | Uses sample permutation to simulate null distributions and calculate robust p-values | ssnappy teer high quality
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