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| gene.results | Gene-specific results from SAFE |
| getCmatrix | Generation of a C matrix |
| safe | Significance Analysis of Function and Expression |
| SAFE-class | Class SAFE |
| safedag | SAFE results displayed in Gene Ontology |
| safeplot | SAFE plot |
| show,SAFE-method | Class SAFE |
| [,SAFE-method | Class SAFE |