API for alyst/MotIV
Motif Identification and Validation
| Global functions | |
|---|---|
| &,filters,filters-method | Man page |
| FOXA | Man page |
| FOXA1_rGADEM | Man page |
| [,motiv,ANY,ANY-method | Man page |
| [,motiv-method | Man page |
| alignments-class | Man page |
| as.data.frame | Man page |
| as.data.frame,motiv-method | Man page |
| as.data.frame-methods | Man page |
| combineMotifs | Man page |
| combineMotifs,motiv,filters-method | Man page |
| combineMotifs,motiv,list-method | Man page |
| combineMotifs-method | Man page |
| cooccurences | Man page |
| exportAsRangedData | Man page |
| exportAsTransfacFile | Man page |
| exportAsTransfacFile,list-method | Man page |
| exportAsTransfacFile,motiv-method | Man page |
| exportAsTransfacFile-methods | Man page |
| filter | Man page |
| filter,motiv,filters-method | Man page |
| filter,motiv,list-method | Man page |
| filter-class | Man page |
| filter-methods | Man page |
| gadem | Man page |
| generateDBScores | Man page |
| getGademPWM | Man page |
| getPWM | Man page |
| getPWM,motiv-method | Man page |
| getPWM-methods | Man page |
| jaspar | Man page |
| jaspar.scores | Man page |
| length,motiv-method | Man page |
| makePWM | Man page |
| matches-class | Man page |
| motifCutree | Man page |
| motifDistances | Man page |
| motifHclust | Man page |
| motifMatch | Man page |
| motiv | Man page |
| motiv-class | Man page |
| names,filter-method | Man page |
| names,filters-method | Man page |
| names,motiv-method | Man page |
| names<-,motiv-method | Man page |
| occurences | Man page |
| plot | Man page |
| plot,motiv,ANY-method | Man page |
| plot,motiv,gadem-method | Man page Man page |
| plot,motiv-method | Man page |
| plot-methods | Man page |
| readDBScores | Man page |
| readGademPWMFile | Man page |
| readPWMfile | Man page |
| seqLogo2 | Man page |
| setFilter | Man page |
| show,filter-method | Man page |
| show,motiv-method | Man page |
| similarity | Man page |
| similarity,list-method | Man page |
| similarity,motiv-method | Man page |
| split,motiv,filters-method | Man page |
| split,motiv,list-method | Man page |
| split-methods | Man page |
| summary,filter-method | Man page |
| summary,filters-method | Man page |
| summary,list-method | Man page |
| summary,motiv-method | Man page |
| transcriptionFactor-class | Man page |
| trimPWMedge | Man page |
| viewAlignments | Man page |
| viewMotifs | Man page |
| viewMotifs,motiv-method | Man page |
| viewMotifs-methods | Man page |
| writeDBScores | Man page |
| |,filters,filters-method | Man page |
