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