&-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 |
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 |