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| .RBPMotif | An S4 class to represent a RBPMotif |
| .SpectrumScore | 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_adj_r_squared | An S4 class to represent a scored spectrum |
| get_adj_r_squared-method | An S4 class to represent a scored spectrum |
| get_consistency_score | An S4 class to represent a scored spectrum |
| get_consistency_score-method | An S4 class to represent a scored spectrum |
| get_consistency_score_n | An S4 class to represent a scored spectrum |
| get_consistency_score_n-method | An S4 class to represent a scored spectrum |
| get_consistency_score_p_value | An S4 class to represent a scored spectrum |
| get_consistency_score_p_value-method | An S4 class to represent a scored spectrum |
| get_heptamers | An S4 class to represent a RBPMotif |
| get_heptamers-method | An S4 class to represent a RBPMotif |
| get_hexamers | An S4 class to represent a RBPMotif |
| get_hexamers-method | An S4 class to represent a RBPMotif |
| get_id | An S4 class to represent a RBPMotif |
| get_id-method | An S4 class to represent a RBPMotif |
| get_iupac | An S4 class to represent a RBPMotif |
| get_iupac-method | An S4 class to represent a RBPMotif |
| get_model_degree | An S4 class to represent a scored spectrum |
| get_model_degree-method | An S4 class to represent a scored spectrum |
| get_model_f_statistic | An S4 class to represent a scored spectrum |
| get_model_f_statistic-method | An S4 class to represent a scored spectrum |
| get_model_f_statistic_p_value | An S4 class to represent a scored spectrum |
| get_model_f_statistic_p_value-method | An S4 class to represent a scored spectrum |
| get_model_residuals | An S4 class to represent a scored spectrum |
| get_model_residuals-method | An S4 class to represent a scored spectrum |
| get_model_slope | An S4 class to represent a scored spectrum |
| get_model_slope-method | An S4 class to represent a scored spectrum |
| get_motifs | Retrieve list of all motifs |
| get_motifs_meta_info | Displays motif meta information. |
| get_motif_by_id | Retrieve motif objects by id |
| get_motif_by_rbp | Retrieve motif objects by gene symbol |
| get_motif_matrix | An S4 class to represent a RBPMotif |
| get_motif_matrix-method | An S4 class to represent a RBPMotif |
| get_ppm | Get Position Probability Matrix (PPM) from motif object |
| get_rbps | An S4 class to represent a RBPMotif |
| get_rbps-method | An S4 class to represent a RBPMotif |
| get_source | An S4 class to represent a RBPMotif |
| get_source-method | An S4 class to represent a RBPMotif |
| get_species | An S4 class to represent a RBPMotif |
| get_species-method | An S4 class to represent a RBPMotif |
| get_type | An S4 class to represent a RBPMotif |
| get_type-method | An S4 class to represent a RBPMotif |
| get_width | An S4 class to represent a RBPMotif |
| get_width-method | An S4 class to represent a RBPMotif |
| init_iupac_lookup_table | Initializes the IUPAC lookup table |
| kmers_enrichment | Example _k_-mer Enrichment Data |
| motifs | Transite Motif Database |
| plot-method | An S4 class to represent a RBPMotif |
| plot-method | An S4 class to represent a scored spectrum |
| p_combine | P-value aggregation |
| RBPMotif-class | An S4 class to represent a RBPMotif |
| 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 |
| show-method | An S4 class to represent a RBPMotif |
| show-method | An S4 class to represent a scored spectrum |
| SpectrumScore-class | An S4 class to represent a scored spectrum |
| subdivide_data | Subdivides Sequences into _n_ Bins |
| toy_motif_matrix | Toy Motif Matrix |
| transite | transite |