# Generated by roxygen2: do not edit by hand

export(GetNearGenes)
export(TCGA.pipe)
export(TF.rank.plot)
export(TFsurvival.plot)
export(addDistNearestTSS)
export(calculateEnrichement)
export(createBigWigDNAmetArray)
export(createIGVtrack)
export(createMAE)
export(createMotifRelevantTfs)
export(createTSVTemplates)
export(get.TFs)
export(get.diff.meth)
export(get.enriched.motif)
export(get.feature.probe)
export(get.pair)
export(get.permu)
export(getExp)
export(getExpSamples)
export(getGeneID)
export(getMet)
export(getMetSamples)
export(getRandomPairs)
export(getRegionNearGenes)
export(getSymbol)
export(getTCGA)
export(getTFBindingSites)
export(getTFtargets)
export(getTSS)
export(heatmapGene)
export(heatmapPairs)
export(metBoxPlot)
export(motif.enrichment.plot)
export(preAssociationProbeFiltering)
export(promoterMeth)
export(render_report)
export(scatter.plot)
export(schematic.plot)
import(ComplexHeatmap)
import(ELMER.data)
import(GenomeInfoDb)
import(Gviz)
import(circlize)
import(ggplot2)
import(lattice)
importFrom(DelayedArray,rowMins)
importFrom(GenomeInfoDb,Seqinfo)
importFrom(GenomicFeatures,transcripts)
importFrom(GenomicRanges,"strand<-")
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,distance)
importFrom(GenomicRanges,distanceToNearest)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,follow)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,nearest)
importFrom(GenomicRanges,precede)
importFrom(GenomicRanges,promoters)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,strand)
importFrom(Gviz,IdeogramTrack)
importFrom(IRanges,IRanges)
importFrom(IRanges,ranges)
importFrom(IRanges,subsetByOverlaps)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(MultiAssayExperiment,"experiments<-")
importFrom(MultiAssayExperiment,MultiAssayExperiment)
importFrom(MultiAssayExperiment,colData)
importFrom(MultiAssayExperiment,experiments)
importFrom(MultiAssayExperiment,sampleMap)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(S4Vectors,values)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,makeSummarizedExperimentFromDataFrame)
importFrom(SummarizedExperiment,rowRanges)
importFrom(TCGAbiolinks,GDCdownload)
importFrom(TCGAbiolinks,GDCprepare)
importFrom(TCGAbiolinks,GDCquery)
importFrom(TCGAbiolinks,GDCquery_clinic)
importFrom(TCGAbiolinks,TCGAVisualize_volcano)
importFrom(TCGAbiolinks,TCGAanalyze_survival)
importFrom(TCGAbiolinks,colDataPrepare)
importFrom(biomaRt,getBM)
importFrom(biomaRt,listDatasets)
importFrom(biomaRt,useEnsembl)
importFrom(biomaRt,useMart)
importFrom(doParallel,registerDoParallel)
importFrom(downloader,download)
importFrom(dplyr,"%>%")
importFrom(dplyr,as_data_frame)
importFrom(dplyr,do)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,group_by_)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,pull)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,top_n)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotation_custom)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_errorbar)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggplot_gtable)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,position_jitter)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,unit)
importFrom(ggpubr,ggscatter)
importFrom(ggpubr,stat_cor)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,col2rgb)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(grDevices,rainbow)
importFrom(graphics,plot)
importFrom(grid,gpar)
importFrom(grid,grobWidth)
importFrom(grid,textGrob)
importFrom(grid,unit.c)
importFrom(gridExtra,arrangeGrob)
importFrom(gridExtra,grid.arrange)
importFrom(lattice,bwplot)
importFrom(magrittr,"%>%")
importFrom(magrittr,add)
importFrom(magrittr,divide_by)
importFrom(magrittr,multiply_by)
importFrom(methods,as)
importFrom(methods,is)
importFrom(parallel,detectCores)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(plyr,.)
importFrom(plyr,a_ply)
importFrom(plyr,adply)
importFrom(plyr,alply)
importFrom(plyr,ddply)
importFrom(plyr,ldply)
importFrom(progress,progress_bar)
importFrom(purrr,reduce)
importFrom(readr,read_csv)
importFrom(readr,read_tsv)
importFrom(readr,write_csv)
importFrom(readr,write_tsv)
importFrom(reshape,melt.data.frame)
importFrom(reshape2,melt)
importFrom(rmarkdown,render)
importFrom(rtracklayer,export.wig)
importFrom(rvest,"%>%")
importFrom(rvest,html_table)
importFrom(scales,scientific)
importFrom(stats,coef)
importFrom(stats,cor.test)
importFrom(stats,dist)
importFrom(stats,fisher.test)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,sd)
importFrom(stats,t.test)
importFrom(stats,wilcox.test)
importFrom(stringr,str_c)
importFrom(stringr,str_split)
importFrom(tibble,as_tibble)
importFrom(tidyr,gather)
importFrom(tidyr,separate_rows)
importFrom(tidyr,unnest)
importFrom(utils,data)
importFrom(utils,head)
importFrom(utils,read.csv)
importFrom(utils,setTxtProgressBar)
importFrom(utils,tail)
importFrom(utils,txtProgressBar)
importFrom(utils,write.csv)
importFrom(utils,write.table)
importFrom(xml2,read_html)
