| safe-package | Significance Analysis of Function and Expression |
| 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 |
| safe.toptable | Category-specific results from SAFE |
| safedag | SAFE results displayed in Gene Ontology |
| safeplot | SAFE plot |
| show-method | Class SAFE |
| [-method | Class SAFE |