| gene.results | Gene-specific results from SAFE |
| getCmatrix | Generation of a C matrix |
| p53.stat | p53 Mutation Status |
| safe | Significance Analysis of Function and Expression |
| SAFE-class | Class SAFE |
| safedag | SAFE results displayed in Gene Ontology |
| safe-internal | Internal SAFE functions |
| safe-package | Significance Analysis of Function and Expression |
| safeplot | SAFE plot |
| safe.toptable | Category-specific results from SAFE |
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