| &-method | Filters Methods |
| alignments-class | Class "alignments" |
| as.data.frame | Coerce to a Data Frame |
| as.data.frame-method | Coerce to a Data Frame |
| as.data.frame-methods | Coerce to a Data Frame |
| combineMotifs | Combine Motifs |
| combineMotifs-method | Combine Motifs |
| cooccurences | Motifs Occurences and Co-occurences |
| exportAsGRanges | Export MotIV Results |
| exportAsRangedData | Export MotIV Results |
| exportAsTransfacFile | Write Transfac Files |
| exportAsTransfacFile-method | Write Transfac Files |
| exportAsTransfacFile-methods | Write Transfac Files |
| filter | Filter Motifs |
| filter-class | Class "filter" |
| filter-method | Filter Motifs |
| filter-methods | Filter Motifs |
| FOXA | Dataset for FOXA1 |
| FOXA1_rGADEM | Dataset for FOXA1 |
| gadem | Dataset for FOXA1 |
| generateDBScores | Database Scores Functions |
| getGademPWM | Recover PWM |
| getPWM | Get PWMs from a motiv object |
| getPWM-method | Get PWMs from a motiv object |
| getPWM-methods | Get PWMs from a motiv object |
| jaspar | Jaspar 2010 Database |
| jaspar.scores | Jaspar 2010 Database |
| length-method | Motiv methods |
| makePWM | Constructing a pwm object |
| matches-class | Class "matches" |
| motifCutree | Clustering PWMs Computation |
| motifDistances | Clustering PWMs Computation |
| motifHclust | Clustering PWMs Computation |
| motifMatch | Motifs Matches Analysis |
| motiv | Motiv methods |
| motiv-class | Class "motiv" |
| names-method | Filters Methods |
| names-method | Motiv methods |
| names<--method | Motiv methods |
| occurences | Motifs Occurences and Co-occurences |
| plot | Plot Motiv |
| plot-method | Plot Motiv |
| plot-methods | Plot Motiv |
| readDBScores | Database Scores Functions |
| readGademPWMFile | Read Gadem File |
| readPWMfile | Read Transfac File |
| seqLogo2 | Plot a sequence logo for a given position weight matrix |
| setFilter | Set Motif Filter |
| show-method | Filters Methods |
| show-method | Motiv methods |
| similarity | Motiv methods |
| similarity-method | Motiv methods |
| split-method | Split Motiv Object |
| split-methods | Split Motiv Object |
| summary-method | Filters Methods |
| summary-method | Motiv methods |
| transcriptionFactor-class | Transcription Factor Class |
| trimPWMedge | Trim PWM edge |
| viewAlignments | Print Motifs Alignments |
| viewMotifs | Print Identified Motifs |
| viewMotifs-method | Print Identified Motifs |
| viewMotifs-methods | Print Identified Motifs |
| writeDBScores | Database Scores Functions |
| [-method | Motiv methods |
| |-method | Filters Methods |