# Generated by roxygen2: do not edit by hand

export(add_splice_part)
export(as_dt_from_s4)
export(as_splice_impact_result)
export(attach_sequences)
export(compare_hit_index)
export(compare_sequence_frame)
export(compare_sequences_alignment)
export(compare_transcript_pairs)
export(enrich_by_db)
export(enrich_by_event)
export(enrich_domains_hypergeo)
export(filter_spliceimpact_hits)
export(get_annotation)
export(get_background)
export(get_comprehensive_annotations)
export(get_di_gene_enrichment)
export(get_differential_inclusion)
export(get_domain_gene_for_enrichment)
export(get_domains)
export(get_enrichment)
export(get_exon_features)
export(get_gene_enrichment)
export(get_hitindex)
export(get_hits_core)
export(get_hits_domain)
export(get_hits_final_view)
export(get_hits_ppi)
export(get_hits_sequence)
export(get_manual_features)
export(get_matched_events_chunked)
export(get_pairs)
export(get_ppi_gene_enrichment)
export(get_ppi_interactions)
export(get_ppi_switches)
export(get_protein_features)
export(get_proximal_shift_from_hits)
export(get_rmats)
export(get_rmats_hit)
export(get_rmats_post_di)
export(get_splicing_impact)
export(get_user_data)
export(get_user_data_post_di)
export(import_di_table)
export(integrated_event_summary)
export(keep_sig_pairs)
export(load_example_data)
export(load_rmats)
export(overview_spicing_comparison)
export(plot_alignment_summary)
export(plot_di_volcano_dt)
export(plot_enriched_domains_counts)
export(plot_length_comparison)
export(plot_ppi_summary)
export(plot_two_transcripts_with_domains_unified)
export(probe_individual_event)
export(spliceimpact_s4_guide)
export(spliceimpact_s4_schema)
import(data.table)
importFrom(BiocParallel,bplapply)
importFrom(Biostrings,AAString)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,readAAStringSet)
importFrom(Biostrings,subseq)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,pintersect)
importFrom(IRanges,IRanges)
importFrom(IRanges,pintersect)
importFrom(IRanges,width)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(data.table,"%chin%")
importFrom(data.table,":=")
importFrom(data.table,CJ)
importFrom(data.table,as.data.table)
importFrom(data.table,copy)
importFrom(data.table,data.table)
importFrom(data.table,dcast)
importFrom(data.table,fifelse)
importFrom(data.table,first)
importFrom(data.table,foverlaps)
importFrom(data.table,frank)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(data.table,getDTthreads)
importFrom(data.table,melt)
importFrom(data.table,rbindlist)
importFrom(data.table,rleid)
importFrom(data.table,setDF)
importFrom(data.table,setDT)
importFrom(data.table,setDTthreads)
importFrom(data.table,setcolorder)
importFrom(data.table,setkey)
importFrom(data.table,setkeyv)
importFrom(data.table,setnames)
importFrom(data.table,setorder)
importFrom(data.table,setorderv)
importFrom(data.table,shift)
importFrom(data.table,tstrsplit)
importFrom(data.table,uniqueN)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,select)
importFrom(dplyr,summarize)
importFrom(ggplot2,aes)
importFrom(ggplot2,after_stat)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,coord_polar)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expand_limits)
importFrom(ggplot2,expansion)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_blank)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_rug)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,position_jitterdodge)
importFrom(ggplot2,position_stack)
importFrom(ggplot2,scale_alpha_identity)
importFrom(ggplot2,scale_color_gradient)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_x_reverse)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,stat_ecdf)
importFrom(ggplot2,stat_summary)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(ggpubr,ggarrange)
importFrom(magrittr,"%>%")
importFrom(methods,is)
importFrom(patchwork,plot_annotation)
importFrom(patchwork,plot_layout)
importFrom(patchwork,wrap_plots)
importFrom(pwalign,alignedPattern)
importFrom(pwalign,alignedSubject)
importFrom(pwalign,nucleotideSubstitutionMatrix)
importFrom(pwalign,pairwiseAlignment)
importFrom(rtracklayer,readGFF)
importFrom(scales,percent)
importFrom(scales,percent_format)
importFrom(scales,rescale)
importFrom(stats,anova)
importFrom(stats,cooks.distance)
importFrom(stats,end)
importFrom(stats,glm)
importFrom(stats,ks.test)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,phyper)
importFrom(stats,quantile)
importFrom(stats,quasibinomial)
importFrom(stats,reorder)
importFrom(stats,setNames)
importFrom(stats,start)
importFrom(stats,t.test)
importFrom(stats,wilcox.test)
importFrom(tidyr,pivot_wider)
importFrom(tools,file_ext)
importFrom(tools,toTitleCase)
importFrom(utils,URLencode)
importFrom(utils,data)
