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| transite-package | transite |
| .RBPMotif | An S4 class to represent a RBPMotif |
| .SpectrumScore | 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 |
| motifHeptamers | An S4 class to represent a RBPMotif |
| motifHeptamers-method | An S4 class to represent a RBPMotif |
| motifHexamers | An S4 class to represent a RBPMotif |
| motifHexamers-method | An S4 class to represent a RBPMotif |
| motifId | An S4 class to represent a RBPMotif |
| motifId-method | An S4 class to represent a RBPMotif |
| motifIUPAC | An S4 class to represent a RBPMotif |
| motifIUPAC-method | An S4 class to represent a RBPMotif |
| motifLength | An S4 class to represent a RBPMotif |
| motifLength-method | An S4 class to represent a RBPMotif |
| motifMatrix | An S4 class to represent a RBPMotif |
| motifMatrix-method | An S4 class to represent a RBPMotif |
| motifRbps | An S4 class to represent a RBPMotif |
| motifRbps-method | An S4 class to represent a RBPMotif |
| motifs | Transite Motif Database |
| motifsMetaInfo | Displays motif meta information. |
| motifSource | An S4 class to represent a RBPMotif |
| motifSource-method | An S4 class to represent a RBPMotif |
| motifSpecies | An S4 class to represent a RBPMotif |
| motifSpecies-method | An S4 class to represent a RBPMotif |
| motifType | An S4 class to represent a RBPMotif |
| motifType-method | An S4 class to represent a RBPMotif |
| pCombine | P-value aggregation |
| permTestGeometricMean | Permutation Test Based Significance of Observed Mean |
| plot-method | An S4 class to represent a RBPMotif |
| plot-method | An S4 class to represent a scored spectrum |
| RBPMotif-class | An S4 class to represent a RBPMotif |
| 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 |
| show-method | An S4 class to represent a RBPMotif |
| show-method | An S4 class to represent a scored spectrum |
| spectrumAdjRSquared | An S4 class to represent a scored spectrum |
| spectrumAdjRSquared-method | An S4 class to represent a scored spectrum |
| spectrumClassifier | Simple spectrum classifier based on empirical thresholds |
| spectrumConsistencyScore | An S4 class to represent a scored spectrum |
| spectrumConsistencyScore-method | An S4 class to represent a scored spectrum |
| spectrumConsistencyScoreN | An S4 class to represent a scored spectrum |
| spectrumConsistencyScoreN-method | An S4 class to represent a scored spectrum |
| spectrumConsistencyScorePValue | An S4 class to represent a scored spectrum |
| spectrumConsistencyScorePValue-method | An S4 class to represent a scored spectrum |
| spectrumDegree | An S4 class to represent a scored spectrum |
| spectrumDegree-method | An S4 class to represent a scored spectrum |
| spectrumFStatistic | An S4 class to represent a scored spectrum |
| spectrumFStatistic-method | An S4 class to represent a scored spectrum |
| spectrumFStatisticPValue | An S4 class to represent a scored spectrum |
| spectrumFStatisticPValue-method | An S4 class to represent a scored spectrum |
| spectrumResiduals | An S4 class to represent a scored spectrum |
| spectrumResiduals-method | An S4 class to represent a scored spectrum |
| SpectrumScore-class | An S4 class to represent a scored spectrum |
| spectrumSlope | An S4 class to represent a scored spectrum |
| spectrumSlope-method | An S4 class to represent a scored spectrum |
| subdivideData | Subdivides Sequences into _n_ Bins |
| toy.motif.matrix | Toy Motif Matrix |
| transite | transite |