# Generated by roxygen2 (4.1.1): do not edit by hand

S3method(as.data.frame,csAnno)
export(annotatePeak)
export(as.GRanges)
export(covplot)
export(downloadGEObedFiles)
export(downloadGSMbedFiles)
export(enrichAnnoOverlap)
export(enrichPeakOverlap)
export(getGEOInfo)
export(getGEOgenomeVersion)
export(getGEOspecies)
export(getPromoters)
export(getSampleFiles)
export(getTagMatrix)
export(overlap)
export(peakHeatmap)
export(plotAnnoBar)
export(plotAnnoPie)
export(plotAnnoPie.csAnno)
export(plotAvgProf)
export(plotAvgProf2)
export(plotChrCov)
export(plotDistToTSS)
export(readPeakFile)
export(seq2gene)
export(shuffle)
export(tagHeatmap)
export(vennpie)
export(vennplot)
export(vennplot.peakfile)
exportClasses(csAnno)
exportMethods(plotAnnoBar)
exportMethods(plotAnnoPie)
exportMethods(plotDistToTSS)
exportMethods(show)
exportMethods(vennpie)
importFrom(AnnotationDbi,get)
importFrom(AnnotationDbi,select)
importFrom(BiocGenerics,image)
importFrom(BiocGenerics,intersect)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,unique)
importFrom(GenomeInfoDb,"seqinfo<-")
importFrom(GenomeInfoDb,intersect)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicFeatures,exonsBy)
importFrom(GenomicFeatures,fiveUTRsByTranscript)
importFrom(GenomicFeatures,genes)
importFrom(GenomicFeatures,intronsByTranscript)
importFrom(GenomicFeatures,threeUTRsByTranscript)
importFrom(GenomicFeatures,transcripts)
importFrom(GenomicFeatures,transcriptsBy)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,strand)
importFrom(GenomicRanges,unlist)
importFrom(IRanges,"end<-")
importFrom(IRanges,"ranges<-")
importFrom(IRanges,"start<-")
importFrom(IRanges,IRanges)
importFrom(IRanges,Views)
importFrom(IRanges,as.vector)
importFrom(IRanges,coverage)
importFrom(IRanges,elementLengths)
importFrom(IRanges,end)
importFrom(IRanges,findOverlaps)
importFrom(IRanges,follow)
importFrom(IRanges,precede)
importFrom(IRanges,ranges)
importFrom(IRanges,slice)
importFrom(IRanges,start)
importFrom(IRanges,subsetByOverlaps)
importFrom(IRanges,viewApply)
importFrom(IRanges,width)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,as.factor)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,runValue)
importFrom(S4Vectors,subjectHits)
importFrom(TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg19.knownGene)
importFrom(boot,boot)
importFrom(boot,boot.ci)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,summarise)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_ribbon)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_brewer)
importFrom(ggplot2,scale_fill_hue)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(gplots,plot.venn)
importFrom(grDevices,colorRampPalette)
importFrom(gtools,permutations)
importFrom(magrittr,"%<>%")
importFrom(magrittr,"%>%")
importFrom(methods,show)
importFrom(parallel,detectCores)
importFrom(parallel,mclapply)
importFrom(plotrix,floating.pie)
importFrom(plyr,.)
importFrom(plyr,ldply)
importFrom(rtracklayer,import.chain)
importFrom(rtracklayer,liftOver)
importMethodsFrom(BiocGenerics,as.data.frame)
importMethodsFrom(BiocGenerics,unlist)
