| $-method | Class '"Enhancers"' |
| $<--method | Class '"Enhancers"' |
| alignment | Output |
| alignmentOne | Get alignment scores |
| coerce | Class '"Enhancers"' |
| coerce-method | Class '"Enhancers"' |
| conservedMotifs | check the conserved motifs in the orthologs |
| distance | Class '"Enhancers"' |
| distance-method | Class '"Enhancers"' |
| distance<- | Class '"Enhancers"' |
| distance<--method | Class '"Enhancers"' |
| Enhancers | Class '"Enhancers"' |
| Enhancers-class | Class '"Enhancers"' |
| genome | Class '"Enhancers"' |
| genome-method | Class '"Enhancers"' |
| genome<- | Class '"Enhancers"' |
| genome<--method | Class '"Enhancers"' |
| getENCODEdata | Download enhancer sequences from ENCODE |
| getSeq-method | Class '"Enhancers"' |
| motifs | Pre-clustered motifs from human and mouse |
| peaks | Class '"Enhancers"' |
| peaks-method | Class '"Enhancers"' |
| peaks<- | Class '"Enhancers"' |
| peaks<--method | Class '"Enhancers"' |
| queryEncode | query data from ENCODE by predefined criteria |
| query_tfbp | Class '"Enhancers"' |
| query_tfbp-method | Class '"Enhancers"' |
| saveAlignments | output alignments |
| searchTFBPS | Transcription Factor Binding Pattern Similarity (TFBPS) search |
| seqinfo-method | Class '"Enhancers"' |
| show-method | Class '"Enhancers"' |
| subset-method | Class '"Enhancers"' |
| subsetByOverlaps-method | Class '"Enhancers"' |
| subsetByOverlpas-method | Class '"Enhancers"' |
| tfbp | Class '"Enhancers"' |
| tfbp-method | Class '"Enhancers"' |