RBPMotif-class          An S4 class to represent a RBPMotif
SpectrumScore-class     An S4 class to represent a scored spectrum
calculate_kmer_enrichment
                        _k_-mer Enrichment between Foreground and
                        Background Sets
calculate_local_consistency
                        Local Consistency Score
calculate_motif_enrichment
                        Binding Site Enrichment Value Calculation
calculate_transcript_mc
                        Motif Enrichment calculation
check_kmers             Check Validity of Set of _k_-mers
classify_spectrum       Simple spectrum classifier based on empirical
                        thresholds
compute_kmer_enrichment
                        _k_-mer Enrichment between Foreground and
                        Background Sets
count_homopolymer_corrected_kmers
                        Correction for Homopolymeric Stretches
create_kmer_motif       Creates Transite motif object from character
                        vector of _k_-mers
create_matrix_motif     Creates Transite motif object from position
                        weight matrix
draw_volcano_plot       _k_-mer Enrichment Volcano Plot
estimate_significance   Permutation Test Based Significance of Observed
                        Mean
estimate_significance_core
                        Significance of Observed Mean
ge                      Toy Gene Expression Data Set
generate_iupac_by_kmers
                        Generates IUPAC code for a character vector of
                        _k_-mers
generate_iupac_by_matrix
                        Generates IUPAC code for motif matrix
generate_kmers          _k_-mer Counts for Sequence Set
generate_kmers_from_iupac
                        Generates all _k_-mers for IUPAC string
generate_permuted_enrichments
                        Generate Random Permutations of the Enrichment
                        Data
geometric_mean          Geometric Mean
get_motif_by_id         Retrieve motif objects by id
get_motif_by_rbp        Retrieve motif objects by gene symbol
get_motifs              Retrieve list of all motifs
get_motifs_meta_info    Displays motif meta information.
get_ppm                 Get Position Probability Matrix (PPM) from
                        motif object
init_iupac_lookup_table
                        Initializes the IUPAC lookup table
kmers_enrichment        Example _k_-mer Enrichment Data
motifs                  Transite Motif Database
p_combine               P-value aggregation
run_kmer_spma           _k_-mer-based Spectrum Motif Analysis
run_kmer_tsma           _k_-mer-based Transcript Set Motif Analysis
run_matrix_spma         Matrix-based Spectrum Motif Analysis
run_matrix_tsma         Matrix-based Transcript Set Motif Analysis
score_sequences         Score Sequences with PWM
score_spectrum          Calculates spectrum scores and creates spectrum
                        plots
score_transcripts       Scores transcripts with position weight
                        matrices
score_transcripts_single_motif
                        Scores transadsadscripts with position weight
                        matrices
set_motifs              Set Transite motif database
subdivide_data          Subdivides Sequences into _n_ Bins
toy_motif_matrix        Toy Motif Matrix
transite                transite
