# Generated by roxygen2: do not edit by hand

export(GeneReguPipe)
export(PECA_TF_enrich)
export(findMotifsInRegions)
export(genBackground)
export(geneOntology)
export(regionConnectTargetGene)
export(tfsEnrichInRegions)
export(tissueOpennessConserve)
export(tissueOpennessSpecificity)
export(unzipAndMergeBed)
exportClasses(EnrichStep)
exportMethods(enrichFindMotifsInRegions)
exportMethods(enrichGenBackground)
exportMethods(enrichGeneOntology)
exportMethods(enrichRegionConnectTargetGene)
exportMethods(enrichSingleSampleReport)
exportMethods(enrichTFsEnrichInRegions)
exportMethods(enrichTissueOpennessConserve)
exportMethods(enrichTissueOpennessSpecificity)
exportMethods(enrichUnzipAndMergeBed)
importFrom(BSgenome,getBSgenome)
importFrom(BiocGenerics,"end<-")
importFrom(BiocGenerics,"score<-")
importFrom(BiocGenerics,"start<-")
importFrom(BiocGenerics,"strand<-")
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicRanges,GRanges)
importFrom(IRanges,IRanges)
importFrom(IRanges,findOverlapPairs)
importFrom(JASPAR2018,JASPAR2018)
importFrom(R.utils,bunzip2)
importFrom(R.utils,gunzip)
importFrom(R.utils,isBzipped)
importFrom(R.utils,isGzipped)
importFrom(S4Vectors,"first<-")
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,"second<-")
importFrom(S4Vectors,first)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,second)
importFrom(TFBSTools,PFMatrix)
importFrom(TFBSTools,PFMatrixList)
importFrom(TFBSTools,getMatrixSet)
importFrom(clusterProfiler,enrichGO)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggpubr,ggarrange)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(heatmap3,heatmap3)
importFrom(magrittr,'%>%')
importFrom(methods,new)
importFrom(motifmatchr,matchMotifs)
importFrom(parallel,makeCluster)
importFrom(parallel,parLapply)
importFrom(parallel,stopCluster)
importFrom(pipeFrame,"input<-")
importFrom(pipeFrame,"output<-")
importFrom(pipeFrame,"param")
importFrom(pipeFrame,"param<-")
importFrom(pipeFrame,Step)
importFrom(pipeFrame,addEdges)
importFrom(pipeFrame,checkAndInstallBSgenome)
importFrom(pipeFrame,checkAndInstallGenomeFa)
importFrom(pipeFrame,checkAndInstallOrgDb)
importFrom(pipeFrame,checkFileCreatable)
importFrom(pipeFrame,checkFileExist)
importFrom(pipeFrame,checkPathExist)
importFrom(pipeFrame,getBasenamePrefix)
importFrom(pipeFrame,getGenome)
importFrom(pipeFrame,getJobDir)
importFrom(pipeFrame,getJobName)
importFrom(pipeFrame,getNextSteps)
importFrom(pipeFrame,getObjsInPipe)
importFrom(pipeFrame,getPathPrefix)
importFrom(pipeFrame,getPrevSteps)
importFrom(pipeFrame,getRef)
importFrom(pipeFrame,getRefDir)
importFrom(pipeFrame,getRefFiles)
importFrom(pipeFrame,getRefRc)
importFrom(pipeFrame,getThreads)
importFrom(pipeFrame,getTmpDir)
importFrom(pipeFrame,getValidGenome)
importFrom(pipeFrame,initPipeFrame)
importFrom(pipeFrame,input)
importFrom(pipeFrame,output)
importFrom(pipeFrame,processing)
importFrom(pipeFrame,runWithFinishCheck)
importFrom(pipeFrame,setGenome)
importFrom(pipeFrame,setJobName)
importFrom(pipeFrame,setPipeName)
importFrom(pipeFrame,setRefDir)
importFrom(pipeFrame,setThreads)
importFrom(pipeFrame,setTmpDir)
importFrom(pipeFrame,stepType)
importFrom(rmarkdown,render)
importFrom(rtracklayer,export.bed)
importFrom(rtracklayer,import)
importFrom(rtracklayer,import.bed)
importFrom(stats,fisher.test)
importFrom(stats,median)
importFrom(stats,p.adjust)
importFrom(stats,t.test)
importFrom(utils,download.file)
importFrom(utils,read.table)
importFrom(utils,write.table)
importMethodsFrom(pipeFrame,checkAllPath)
importMethodsFrom(pipeFrame,checkRequireParam)
importMethodsFrom(pipeFrame,clearStepCache)
importMethodsFrom(pipeFrame,getAutoPath)
importMethodsFrom(pipeFrame,getParam)
importMethodsFrom(pipeFrame,getParamItems)
importMethodsFrom(pipeFrame,getParamMD5Path)
importMethodsFrom(pipeFrame,getStepWorkDir)
importMethodsFrom(pipeFrame,init)
importMethodsFrom(pipeFrame,isReady)
importMethodsFrom(pipeFrame,stepID)
importMethodsFrom(pipeFrame,stepName)
importMethodsFrom(pipeFrame,writeLog)
