API for jianhong/enhancerHomologSearch
Identification of putative mammalian orthologs to given enhancer
| Global functions | |
|---|---|
| $,Enhancers-method | Man page |
| $<-,Enhancers-method | Man page |
| Enhancers | Man page Source code |
| Enhancers-class | Man page |
| RClustalW | Source code |
| RMuscle | Source code |
| TFBPscore | Source code |
| alignment | Man page Source code |
| alignmentOne | Man page Source code |
| checkMotifCons | Source code |
| checkPWMs | Source code |
| checkQuerySubject | Source code |
| checkSubject | Source code |
| checkSubstitutionMatrix | Source code |
| checkTFBPs | Source code |
| coerce | Man page |
| coerce,Enhancers,GRanges-method | Man page |
| conservedMotifs | Man page Source code |
| distance | Man page |
| distance,Enhancers,ANY-method | Man page |
| distance,Enhancers-method | Man page |
| distance<- | Man page |
| distance<-,Enhancers,ANY-method | Man page |
| distance<-,Enhancers-method | Man page |
| genome | Man page |
| genome,Enhancers-method | Man page |
| genome<- | Man page |
| genome<-,Enhancers,BSgenome-method | Man page |
| genome<-,Enhancers-method | Man page |
| getENCODEdata | Man page Source code |
| getSeq,Enhancers-method | Man page |
| guessAssembly | Source code |
| motifs | Man page |
| msa | Source code |
| parseAln | Source code |
| peaks | Man page |
| peaks,Enhancers-method | Man page |
| peaks<- | Man page |
| peaks<-,Enhancers,GRanges-method | Man page |
| peaks<-,Enhancers-method | Man page |
| prepareClustalWparams | Source code |
| prepareMuscleparams | Source code |
| queryEncode | Man page Source code |
| query_tfbp | Man page |
| query_tfbp,Enhancers,ANY-method | Man page |
| query_tfbp,Enhancers-method | Man page |
| rushuffle | Source code |
| saveAlignments | Man page Source code |
| searchTFBP | Source code |
| searchTFBPS | Man page Source code |
| seqinfo,Enhancers-method | Man page |
| show,Enhancers-method | Man page |
| shuffle | Man page Source code |
| splitStrByBlock | Source code |
| subset,Enhancers-method | Man page |
| subsetByOverlaps,Enhancers,ANY-method | Man page |
| subsetByOverlpas,Enhancers-method | Man page |
| subsetTFBP | Source code |
| tfbp | Man page |
| tfbp,Enhancers,ANY-method | Man page |
| tfbp,Enhancers-method | Man page |
| write.phylip_html | Source code |
