# Generated by roxygen2: do not edit by hand

export(calculate_kmer_enrichment)
export(calculate_local_consistency)
export(calculate_motif_enrichment)
export(calculate_transcript_mc)
export(check_kmers)
export(classify_spectrum)
export(compute_kmer_enrichment)
export(create_kmer_motif)
export(create_matrix_motif)
export(draw_volcano_plot)
export(estimate_significance)
export(estimate_significance_core)
export(generate_iupac_by_kmers)
export(generate_iupac_by_matrix)
export(generate_kmers)
export(generate_kmers_from_iupac)
export(generate_permuted_enrichments)
export(geometric_mean)
export(get_motif_by_id)
export(get_motif_by_rbp)
export(get_motifs)
export(get_motifs_meta_info)
export(get_ppm)
export(init_iupac_lookup_table)
export(p_combine)
export(run_kmer_spma)
export(run_kmer_tsma)
export(run_matrix_spma)
export(run_matrix_tsma)
export(score_sequences)
export(score_spectrum)
export(score_transcripts)
export(set_motifs)
export(subdivide_data)
exportClasses(RBPMotif)
exportClasses(SpectrumScore)
exportMethods(get_adj_r_squared)
exportMethods(get_consistency_score)
exportMethods(get_consistency_score_n)
exportMethods(get_consistency_score_p_value)
exportMethods(get_heptamers)
exportMethods(get_hexamers)
exportMethods(get_id)
exportMethods(get_iupac)
exportMethods(get_model_degree)
exportMethods(get_model_f_statistic)
exportMethods(get_model_f_statistic_p_value)
exportMethods(get_model_residuals)
exportMethods(get_model_slope)
exportMethods(get_motif_matrix)
exportMethods(get_rbps)
exportMethods(get_source)
exportMethods(get_species)
exportMethods(get_type)
exportMethods(get_width)
exportMethods(plot)
importFrom(BiocGenerics,width)
importFrom(Biostrings,BString)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,IUPAC_CODE_MAP)
importFrom(Biostrings,RNAStringSet)
importFrom(Biostrings,maskMotif)
importFrom(Biostrings,maxScore)
importFrom(Biostrings,oligonucleotideFrequency)
importFrom(GenomicRanges,gaps)
importFrom(Rcpp,sourceCpp)
importFrom(TFMPvalue,TFMpv2sc)
importFrom(dplyr,arrange)
importFrom(dplyr,filter)
importFrom(dplyr,select)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_area)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggplot_gtable)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_alpha_manual)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_gradient2)
importFrom(ggplot2,scale_size_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggseqlogo,ggseqlogo)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(gridExtra,arrangeGrob)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setClassUnion)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(methods,signature)
importFrom(parallel,clusterExport)
importFrom(parallel,makeCluster)
importFrom(parallel,parLapply)
importFrom(parallel,stopCluster)
importFrom(scales,pretty_breaks)
importFrom(stats,binom.test)
importFrom(stats,chisq.test)
importFrom(stats,fisher.test)
importFrom(stats,lm)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,pf)
importFrom(stats,pnorm)
importFrom(stats,poly)
importFrom(stats,predict)
importFrom(stats,pt)
importFrom(stats,qnorm)
importFrom(stats,sd)
importFrom(utils,data)
useDynLib(transite)
