RBPMotif-class          An S4 class to represent a RBPMotif
SpectrumScore-class     An S4 class to represent a scored spectrum
calculateKmerEnrichment
                        _k_-mer Enrichment between Foreground and
                        Background Sets
calculateKmerScores     _k_-mer Score Calculation
calculateLocalConsistency
                        Local Consistency Score
calculateMotifEnrichment
                        Binding Site Enrichment Value Calculation
calculateTranscriptMC   Motif Enrichment calculation
checkKmers              Check Validity of Set of _k_-mers
computeKmerEnrichment   _k_-mer Enrichment between Foreground and
                        Background Sets
computeMotifScore       Motif Score Algorithm
createKmerMotif         Creates Transite motif object from character
                        vector of _k_-mers
createMatrixMotif       Creates Transite motif object from position
                        weight matrix
drawVolcanoPlot         _k_-mer Enrichment Volcano Plot
empiricalEnrichmentMeanCDF
                        Significance of Observed Mean
ge                      Toy Gene Expression Data Set
generateIUPACByKmers    Generates IUPAC code for a character vector of
                        _k_-mers
generateIUPACByMatrix   Generates IUPAC code for motif matrix
generateKmers           _k_-mer Counts for Sequence Set
generateKmersFromIUPAC
                        Generates all _k_-mers for IUPAC string
generatePermutedEnrichments
                        Generate Random Permutations of the Enrichment
                        Data
geometricMean           Geometric Mean
getMotifById            Retrieve motif objects by id
getMotifByRBP           Retrieve motif objects by gene symbol
getMotifs               Retrieve list of all motifs
getPPM                  Get Position Probability Matrix (PPM) from
                        motif object
homopolymerCorrection   Correction for Homopolymeric Stretches
initIUPAClookupTable    Initializes the IUPAC lookup table
kmers.enrichment        Example _k_-mer Enrichment Data
lookupKmerScores        _k_-mer Score Lookup Table Access Function
motifs                  Transite Motif Database
motifsMetaInfo          Displays motif meta information.
pCombine                P-value aggregation
permTestGeometricMean   Permutation Test Based Significance of Observed
                        Mean
runKmerSPMA             _k_-mer-based Spectrum Motif Analysis
runKmerTSMA             _k_-mer-based Transcript Set Motif Analysis
runMatrixSPMA           Matrix-based Spectrum Motif Analysis
runMatrixTSMA           Matrix-based Transcript Set Motif Analysis
scoreSequences          Score Sequences with PWM
scoreSpectrum           Calculates spectrum scores and creates spectrum
                        plots
scoreTranscripts        Scores transcripts with position weight
                        matrices
scoreTranscriptsSingleMotif
                        Scores transadsadscripts with position weight
                        matrices
setMotifs               Set Transite motif database
spectrumClassifier      Simple spectrum classifier based on empirical
                        thresholds
subdivideData           Subdivides Sequences into _n_ Bins
toy.motif.matrix        Toy Motif Matrix
transite                transite
