transite-package	transite
.RBPMotif	RBPMotif-class
.SpectrumScore	SpectrumScore-class
calculate_kmer_enrichment	calculate_kmer_enrichment
calculate_local_consistency	calculate_local_consistency
calculate_motif_enrichment	calculate_motif_enrichment
calculate_transcript_mc	calculate_transcript_mc
check_kmers	check_kmers
classify_spectrum	classify_spectrum
compute_kmer_enrichment	compute_kmer_enrichment
count_homopolymer_corrected_kmers	count_homopolymer_corrected_kmers
create_kmer_motif	create_kmer_motif
create_kmer_origin_list	create_kmer_origin_list
create_matrix_motif	create_matrix_motif
draw_volcano_plot	draw_volcano_plot
estimate_significance	estimate_significance
estimate_significance_core	estimate_significance_core
ge	ge
generate_iupac_by_kmers	generate_iupac_by_kmers
generate_iupac_by_matrix	generate_iupac_by_matrix
generate_kmers	generate_kmers
generate_kmers_from_iupac	generate_kmers_from_iupac
generate_permuted_enrichments	generate_permuted_enrichments
geometric_mean	geometric_mean
get_adj_r_squared	SpectrumScore-class
get_adj_r_squared,SpectrumScore-method	SpectrumScore-class
get_consistency_score	SpectrumScore-class
get_consistency_score,SpectrumScore-method	SpectrumScore-class
get_consistency_score_n	SpectrumScore-class
get_consistency_score_n,SpectrumScore-method	SpectrumScore-class
get_consistency_score_p_value	SpectrumScore-class
get_consistency_score_p_value,SpectrumScore-method	SpectrumScore-class
get_heptamers	RBPMotif-class
get_heptamers,RBPMotif-method	RBPMotif-class
get_hexamers	RBPMotif-class
get_hexamers,RBPMotif-method	RBPMotif-class
get_id	RBPMotif-class
get_id,RBPMotif-method	RBPMotif-class
get_iupac	RBPMotif-class
get_iupac,RBPMotif-method	RBPMotif-class
get_model_degree	SpectrumScore-class
get_model_degree,SpectrumScore-method	SpectrumScore-class
get_model_f_statistic	SpectrumScore-class
get_model_f_statistic,SpectrumScore-method	SpectrumScore-class
get_model_f_statistic_p_value	SpectrumScore-class
get_model_f_statistic_p_value,SpectrumScore-method	SpectrumScore-class
get_model_residuals	SpectrumScore-class
get_model_residuals,SpectrumScore-method	SpectrumScore-class
get_model_slope	SpectrumScore-class
get_model_slope,SpectrumScore-method	SpectrumScore-class
get_motifs	get_motifs
get_motifs_meta_info	get_motifs_meta_info
get_motif_by_id	get_motif_by_id
get_motif_by_rbp	get_motif_by_rbp
get_motif_matrix	RBPMotif-class
get_motif_matrix,RBPMotif-method	RBPMotif-class
get_ppm	get_ppm
get_rbps	RBPMotif-class
get_rbps,RBPMotif-method	RBPMotif-class
get_source	RBPMotif-class
get_source,RBPMotif-method	RBPMotif-class
get_species	RBPMotif-class
get_species,RBPMotif-method	RBPMotif-class
get_type	RBPMotif-class
get_type,RBPMotif-method	RBPMotif-class
get_width	RBPMotif-class
get_width,RBPMotif-method	RBPMotif-class
init_iupac_lookup_table	init_iupac_lookup_table
kmers_enrichment	kmers_enrichment
motifs	motifs
plot,SpectrumScore,ANY-method	SpectrumScore-class
plot,SpectrumScore-method	SpectrumScore-class
p_combine	p_combine
RBPMotif-class	RBPMotif-class
run_kmer_spma	run_kmer_spma
run_kmer_tsma	run_kmer_tsma
run_matrix_spma	run_matrix_spma
run_matrix_tsma	run_matrix_tsma
score_sequences	score_sequences
score_spectrum	score_spectrum
score_transcripts	score_transcripts
score_transcripts_single_motif	score_transcripts_single_motif
set_motifs	set_motifs
show,RBPMotif-method	RBPMotif-class
show,SpectrumScore-method	SpectrumScore-class
SpectrumScore-class	SpectrumScore-class
subdivide_data	subdivide_data
toy_motif_matrix	toy_motif_matrix
transite	transite
