NAMESPACE

# Generated by roxygen2: do not edit by hand

export("%>%")
export(TE_analysis)
export(TE_differential_analysis)
export(codon_occupancy_plot)
export(codon_scatter_plot)
export(construct_ribotrans)
export(construct_serp)
export(cor_plot)
export(digestion_site_plot)
export(do_boot)
export(do_offset_correction)
export(ecdf_plot)
export(enrich_analysis)
export(enrichment_metagene_plot)
export(enrichment_plot1)
export(enrichment_plot2)
export(export_genome_occupancy)
export(feature_plot)
export(find_strong_peaks)
export(find_weak_peaks)
export(frame_plot)
export(gene_differential_analysis)
export(generate_kmers)
export(generate_summary)
export(genome_trans_plot)
export(getCoverage)
export(getCoverageGenome)
export(getOccupancy)
export(getOccupancyGenome)
export(get_aa_table)
export(get_codon_from_site)
export(get_counts)
export(get_coverage)
export(get_log_ratio_mat)
export(get_longest_transcript)
export(get_normalized_reads)
export(get_occupancy)
export(get_pausing_sites)
export(get_scaled_occupancy)
export(get_transcript_sequence)
export(length_plot)
export(logo_plot)
export(metagene_plot)
export(motif_occupancy)
export(multi_peptide_occupancy)
export(peptide_scatter_plot)
export(period_plot)
export(plogo_plot)
export(polarity_plot)
export(prepareTransInfo)
export(prepareTransInfo_forGenome)
export(prepare_transcipt_file)
export(pyExtractSeq)
export(relative_dist_plot)
export(relative_heatmap_plot)
export(relative_motif_occupancy)
export(relative_motif_plot)
export(relative_offset_plot)
export(ribotrans)
export(serp)
export(smoothEachPosition)
export(subset_data)
export(theme_ribo)
export(to_position_matrix)
export(trans_plot)
export(trans_plot2)
export(trim_adaptors)
export(vocalno_plot)
export(whole_metagene_plot)
exportClasses(ribotrans)
exportClasses(serp)
exportMethods(TE_analysis)
exportMethods(TE_differential_analysis)
exportMethods(codon_occupancy_plot)
exportMethods(digestion_site_plot)
exportMethods(enrichment_metagene_plot)
exportMethods(enrichment_plot1)
exportMethods(enrichment_plot2)
exportMethods(export_genome_occupancy)
exportMethods(feature_plot)
exportMethods(find_strong_peaks)
exportMethods(find_weak_peaks)
exportMethods(frame_plot)
exportMethods(gene_differential_analysis)
exportMethods(generate_summary)
exportMethods(genome_trans_plot)
exportMethods(get_codon_from_site)
exportMethods(get_counts)
exportMethods(get_coverage)
exportMethods(get_normalized_reads)
exportMethods(get_occupancy)
exportMethods(get_pausing_sites)
exportMethods(get_scaled_occupancy)
exportMethods(length_plot)
exportMethods(metagene_plot)
exportMethods(motif_occupancy)
exportMethods(multi_peptide_occupancy)
exportMethods(period_plot)
exportMethods(polarity_plot)
exportMethods(relative_dist_plot)
exportMethods(relative_heatmap_plot)
exportMethods(relative_motif_occupancy)
exportMethods(relative_offset_plot)
exportMethods(subset_data)
exportMethods(trans_plot)
exportMethods(trans_plot2)
exportMethods(whole_metagene_plot)
import(Rcpp)
import(RcppArmadillo)
import(dplyr)
import(ggplot2)
import(ggside)
import(methods)
importFrom(Biostrings,AAStringSet)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,GENETIC_CODE)
importFrom(Biostrings,RNAStringSet)
importFrom(Biostrings,consensusMatrix)
importFrom(Biostrings,getSeq)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,translate)
importFrom(Biostrings,vmatchPattern)
importFrom(Biostrings,width)
importFrom(Biostrings,writeXStringSet)
importFrom(GenomicFeatures,extractTranscriptSeqs)
importFrom(GenomicFeatures,makeTxDbFromGRanges)
importFrom(GenomicRanges,GRanges)
importFrom(IRanges,IRanges)
importFrom(IRanges,findOverlaps)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,FaFile)
importFrom(Rsamtools,PileupParam)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,idxstatsBam)
importFrom(Rsamtools,indexFa)
importFrom(Rsamtools,pileup)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(data.table,`:=`)
importFrom(data.table,as.data.table)
importFrom(data.table,fifelse)
importFrom(data.table,rleid)
importFrom(data.table,tstrsplit)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,case_when)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,if_else)
importFrom(dplyr,inner_join)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,slice_max)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(fastplyr,f_arrange)
importFrom(fastplyr,f_filter)
importFrom(fastplyr,f_full_join)
importFrom(fastplyr,f_group_by)
importFrom(fastplyr,f_inner_join)
importFrom(fastplyr,f_left_join)
importFrom(fastplyr,f_select)
importFrom(fastplyr,f_slice_head)
importFrom(fastplyr,f_summarise)
importFrom(ggh4x,facet_grid2)
importFrom(ggh4x,facet_wrap2)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_label)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_path)
importFrom(ggplot2,geom_ribbon)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,position_dodge2)
importFrom(ggplot2,scale_fill_brewer)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggside,geom_xsidesegment)
importFrom(ggside,ggside)
importFrom(ggside,scale_xsidey_continuous)
importFrom(magrittr,"%>%")
importFrom(methods,new)
importFrom(parallel,detectCores)
importFrom(purrr,map)
importFrom(purrr,map_df)
importFrom(scales,label_log)
importFrom(stats,density)
importFrom(stats,fft)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(utils,modifyList)
importFrom(utils,packageDescription)
useDynLib(riboTransVis, .registration = TRUE)