# Generated by roxygen2: do not edit by hand

export(aov_TukeyHSD)
export(check_constraints)
export(custom_TxDb_from_GTF)
export(draw_boxplot_by_factor)
export(draw_boxplot_wo_outlier)
export(draw_combo_plot)
export(draw_locus_profile)
export(draw_matrix_heatmap)
export(draw_mean_se_barplot)
export(draw_quantile_plot)
export(draw_rank_plot)
export(draw_region_landmark)
export(draw_region_name)
export(draw_region_profile)
export(draw_stacked_plot)
export(draw_stacked_profile)
export(effective_size)
export(extract_longest_tx)
export(filter_by_nonoverlaps_stranded)
export(filter_by_overlaps_nonstranded)
export(filter_by_overlaps_stranded)
export(gene2tx)
export(get_genomic_feature_coordinates)
export(get_targeted_genes)
export(get_txdb_features)
export(gr2df)
export(handle_bam)
export(handle_bed)
export(handle_bedGraph)
export(handle_bw)
export(handle_input)
export(handle_wig)
export(make_subTxDb_from_GTF)
export(overlap_pair)
export(overlap_quad)
export(overlap_triple)
export(parallel_countOverlaps)
export(parallel_scoreMatrixBin)
export(plot_5parts_metagene)
export(plot_bam_correlation)
export(plot_locus)
export(plot_locus_with_random)
export(plot_overlap_bed)
export(plot_overlap_genes)
export(plot_peak_annotation)
export(plot_region)
export(plot_start_end)
export(plot_start_end_with_random)
export(prepare_3parts_genomic_features)
export(prepare_5parts_genomic_features)
export(process_scoreMatrix)
export(rank_rows)
export(rm_outlier)
export(setImportParams)
export(set_seqinfo)
export(start_parallel)
export(stop_parallel)
import(ggplot2)
import(methods)
importFrom(BiocGenerics,"end<-")
importFrom(BiocGenerics,"score<-")
importFrom(BiocGenerics,"start<-")
importFrom(BiocGenerics,"strand<-")
importFrom(BiocGenerics,Reduce)
importFrom(BiocGenerics,append)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,score)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,type)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,pheatmap)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicFeatures,cdsBy)
importFrom(GenomicFeatures,exonsBy)
importFrom(GenomicFeatures,fiveUTRsByTranscript)
importFrom(GenomicFeatures,genes)
importFrom(GenomicFeatures,intronsByTranscript)
importFrom(GenomicFeatures,threeUTRsByTranscript)
importFrom(GenomicFeatures,transcriptLengths)
importFrom(GenomicFeatures,transcripts)
importFrom(GenomicRanges,"mcols<-")
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,countOverlaps)
importFrom(GenomicRanges,coverage)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,flank)
importFrom(GenomicRanges,granges)
importFrom(GenomicRanges,grglist)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,narrow)
importFrom(GenomicRanges,nearest)
importFrom(GenomicRanges,promoters)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,setdiff)
importFrom(GenomicRanges,shift)
importFrom(GenomicRanges,tileGenome)
importFrom(GenomicRanges,trim)
importFrom(IRanges,mergeByOverlaps)
importFrom(IRanges,width)
importFrom(RCAS,importGtf)
importFrom(RCAS,queryGff)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,idxstatsBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,testPairedEndBam)
importFrom(Seqinfo,"seqinfo<-")
importFrom(Seqinfo,"seqlevels<-")
importFrom(Seqinfo,"seqnames<-")
importFrom(Seqinfo,Seqinfo)
importFrom(Seqinfo,seqinfo)
importFrom(Seqinfo,seqlengths)
importFrom(Seqinfo,seqlevels)
importFrom(Seqinfo,seqnames)
importFrom(VennDiagram,draw.pairwise.venn)
importFrom(VennDiagram,draw.quad.venn)
importFrom(VennDiagram,draw.triple.venn)
importFrom(circlize,colorRamp2)
importFrom(circlize,read.chromInfo)
importFrom(cowplot,draw_label)
importFrom(cowplot,draw_plot)
importFrom(cowplot,ggdraw)
importFrom(cowplot,plot_grid)
importFrom(dplyr,"%>%")
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,count)
importFrom(dplyr,desc)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,inner_join)
importFrom(dplyr,lead)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,n_distinct)
importFrom(dplyr,rename_with)
importFrom(dplyr,select)
importFrom(dplyr,summarize)
importFrom(edgeR,calcNormFactors)
importFrom(genomation,ScoreMatrixBin)
importFrom(genomation,annotateWithFeatures)
importFrom(ggplotify,as.grob)
importFrom(ggpubr,ggtexttable)
importFrom(ggpubr,tab_add_title)
importFrom(ggpubr,ttheme)
importFrom(ggsci,pal_npg)
importFrom(ggsci,scale_color_npg)
importFrom(ggsci,scale_fill_npg)
importFrom(ggsignif,geom_signif)
importFrom(grDevices,dev.list)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,abline)
importFrom(graphics,boxplot)
importFrom(graphics,hist)
importFrom(graphics,pairs)
importFrom(graphics,panel.smooth)
importFrom(graphics,par)
importFrom(graphics,points)
importFrom(graphics,rect)
importFrom(graphics,strwidth)
importFrom(graphics,text)
importFrom(grid,gpar)
importFrom(grid,grid.draw)
importFrom(grid,grid.grabExpr)
importFrom(grid,grid.newpage)
importFrom(grid,grid.text)
importFrom(parallel,clusterApply)
importFrom(parallel,clusterExport)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,parLapply)
importFrom(parallel,stopCluster)
importFrom(plyranges,filter_by_overlaps)
importFrom(rtracklayer,asBED)
importFrom(rtracklayer,export.bed)
importFrom(rtracklayer,import.bw)
importFrom(rtracklayer,wigToBigWig)
importFrom(scales,percent)
importFrom(scales,rescale)
importFrom(stats,TukeyHSD)
importFrom(stats,aggregate)
importFrom(stats,aov)
importFrom(stats,approx)
importFrom(stats,as.formula)
importFrom(stats,biplot)
importFrom(stats,cor)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,ecdf)
importFrom(stats,hclust)
importFrom(stats,heatmap)
importFrom(stats,ks.test)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,prcomp)
importFrom(stats,qqplot)
importFrom(stats,quantile)
importFrom(stats,reorder)
importFrom(stats,sd)
importFrom(stats,smooth.spline)
importFrom(stats,t.test)
importFrom(stats,wilcox.test)
importFrom(tidyr,pivot_longer)
importFrom(txdbmaker,makeTxDbFromGRanges)
importFrom(utils,combn)
importFrom(utils,data)
importFrom(utils,head)
importFrom(utils,object.size)
importFrom(utils,read.delim)
importFrom(utils,read.delim2)
importFrom(utils,read.table)
importFrom(utils,tail)
importFrom(utils,type.convert)
importFrom(utils,write.table)
importFrom(viridis,scale_fill_viridis)
importFrom(viridis,viridis)
