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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(atacPipe)
export(atacPipe2)
export(atacRepsPipe)
export(atacRepsPipe2)
export(atacSCUnzipAndMerge)
export(atacUnzipAndMerge)
export(atacscCellFilter)
export(atacscQC)
export(bam2bed)
export(bamsort)
export(bedToBigWig)
export(bedUtils)
export(bowtie2Mapping)
export(cutsitecount)
export(extractcutsite)
export(findAdapter)
export(fragLenDistr)
export(fripQC)
export(getMotifInfo)
export(goanalysis)
export(libComplexQC)
export(motifscan)
export(motifscanpair)
export(peakCalling)
export(peakCallingMACS2)
export(peakQC)
export(peakanno)
export(peakcomp)
export(qcreport)
export(removeAdapter)
export(renamer)
export(sam2bam)
export(samToBed)
export(scBowtie2Mapping)
export(scFindAdapter)
export(scRemoveAdapter)
export(scRenamer)
export(scSam2bam)
export(scUnzipAndMerge)
export(snpanno)
export(testPeakCallingMACS2)
export(tssQC)
export(unzipAndMerge)
exportClasses(ATACProc)
exportClasses(Fragment)
exportMethods(atacBam2Bed)
exportMethods(atacBamSort)
exportMethods(atacBedToBigWig)
exportMethods(atacBedUtils)
exportMethods(atacBowtie2Mapping)
exportMethods(atacCutSiteCount)
exportMethods(atacExtractCutSite)
exportMethods(atacFindAdapter)
exportMethods(atacFragLenDistr)
exportMethods(atacFripQC)
exportMethods(atacGOAnalysis)
exportMethods(atacLibComplexQC)
exportMethods(atacMotifScan)
exportMethods(atacMotifScanPair)
exportMethods(atacPeakAnno)
exportMethods(atacPeakCalling)
exportMethods(atacPeakCallingMACS2)
exportMethods(atacPeakComp)
exportMethods(atacPeakQC)
exportMethods(atacQCReport)
exportMethods(atacRemoveAdapter)
exportMethods(atacRenamer)
exportMethods(atacSCBowtie2Mapping)
exportMethods(atacSCCellFilter)
exportMethods(atacSCFindAdapter)
exportMethods(atacSCQC)
exportMethods(atacSCRemoveAdapter)
exportMethods(atacSCRenamer)
exportMethods(atacSCSam2Bam)
exportMethods(atacSNPAnno)
exportMethods(atacSam2Bam)
exportMethods(atacSamToBed)
exportMethods(atacSingleRepReport)
exportMethods(atacTSSQC)
import(IRanges)
import(Rsamtools)
import(S4Vectors)
import(methods)
import(tools)
importClassesFrom(Matrix,dgCMatrix)
importFrom(AnnotationDbi,loadDb)
importFrom(AnnotationDbi,saveDb)
importFrom(BSgenome,available.genomes)
importFrom(BSgenome,getBSgenome)
importFrom(BSgenome,installed.genomes)
importFrom(BiocGenerics,counts)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,subset)
importFrom(BiocGenerics,which)
importFrom(BiocGenerics,width)
importFrom(BiocManager,install)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,alphabetFrequency)
importFrom(Biostrings,injectHardMask)
importFrom(Biostrings,masks)
importFrom(Biostrings,writeXStringSet)
importFrom(ChIPseeker,annotatePeak)
importFrom(ChIPseeker,plotAnnoPie)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb,keepStandardChromosomes)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(GenomicFeatures,makeTxDbFromUCSC)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,coverage)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,sort.GenomicRanges)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,strand)
importFrom(GenomicRanges,trim)
importFrom(GenomicRanges,width)
importFrom(IRanges,"ranges<-")
importFrom(IRanges,IRanges)
importFrom(IRanges,ranges)
importFrom(IRanges,subsetByOverlaps)
importFrom(IRanges,width)
importFrom(JASPAR2018,JASPAR2018)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,rowMeans)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,writeMM)
importFrom(R.utils,bunzip2)
importFrom(R.utils,getAbsolutePath)
importFrom(R.utils,gunzip)
importFrom(R.utils,gzip)
importFrom(R.utils,isBzipped)
importFrom(R.utils,isGzipped)
importFrom(Rbowtie2,bowtie2)
importFrom(Rbowtie2,bowtie2_build)
importFrom(Rbowtie2,identify_adapters)
importFrom(Rbowtie2,remove_adapters)
importFrom(Rcpp,evalCpp)
importFrom(Rcpp,sourceCpp)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,TabixFile)
importFrom(Rsamtools,bgzip)
importFrom(Rsamtools,indexTabix)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanTabix)
importFrom(Rsamtools,seqnamesTabix)
importFrom(Rsamtools,testPairedEndBam)
importFrom(S4Vectors,elementNROWS)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,runLength)
importFrom(S4Vectors,runValue)
importFrom(SeuratObject,Cells)
importFrom(SeuratObject,DefaultAssay)
importFrom(SeuratObject,Idents)
importFrom(SeuratObject,RowMergeSparseMatrices)
importFrom(ShortRead,FastqSampler)
importFrom(ShortRead,alphabetByCycle)
importFrom(ShortRead,readFasta)
importFrom(ShortRead,sread)
importFrom(ShortRead,tables)
importFrom(ShortRead,yield)
importFrom(TFBSTools,PFMatrix)
importFrom(TFBSTools,PFMatrixList)
importFrom(TFBSTools,as.matrix)
importFrom(TFBSTools,getMatrixSet)
importFrom(TFBSTools,name)
importFrom(TFBSTools,toPWM)
importFrom(VennDiagram,draw.pairwise.venn)
importFrom(VennDiagram,venn.diagram)
importFrom(biovizBase,crunch)
importFrom(clusterProfiler,enrichGO)
importFrom(corrplot,corrplot)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(data.table,merge.data.table)
importFrom(digest,digest)
importFrom(dplyr,full_join)
importFrom(fastmatch,fmatch)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_path)
importFrom(ggplot2,geom_ribbon)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.new)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,box)
importFrom(graphics,layout)
importFrom(graphics,matplot)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,rect)
importFrom(graphics,strheight)
importFrom(graphics,strwidth)
importFrom(graphics,text)
importFrom(grid,grid.draw)
importFrom(grid,grid.newpage)
importFrom(igraph,"vertex.attributes<-")
importFrom(igraph,are.connected)
importFrom(igraph,graph)
importFrom(igraph,vertex.attributes)
importFrom(knitr,knit)
importFrom(magrittr,"%>%")
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,slot)
importFrom(motifmatchr,matchMotifs)
importFrom(parallel,makeCluster)
importFrom(parallel,mclapply)
importFrom(parallel,parLapply)
importFrom(parallel,stopCluster)
importFrom(pbapply,pblapply)
importFrom(pipeFrame,"input<-")
importFrom(pipeFrame,"output<-")
importFrom(pipeFrame,"param")
importFrom(pipeFrame,"param<-")
importFrom(pipeFrame,"property")
importFrom(pipeFrame,"property<-")
importFrom(pipeFrame,"report")
importFrom(pipeFrame,"report<-")
importFrom(pipeFrame,Step)
importFrom(pipeFrame,addEdges)
importFrom(pipeFrame,addFileSuffix)
importFrom(pipeFrame,checkAndInstallBSgenome)
importFrom(pipeFrame,checkAndInstallGenomeFa)
importFrom(pipeFrame,checkAndInstallOrgDb)
importFrom(pipeFrame,checkAndInstallTxDb)
importFrom(pipeFrame,checkFileCreatable)
importFrom(pipeFrame,checkFileExist)
importFrom(pipeFrame,checkPathExist)
importFrom(pipeFrame,genReport)
importFrom(pipeFrame,getBasenamePrefix)
importFrom(pipeFrame,getGenome)
importFrom(pipeFrame,getJobDir)
importFrom(pipeFrame,getJobName)
importFrom(pipeFrame,getNextSteps)
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,ignoreCheck)
importFrom(pipeFrame,initPipeFrame)
importFrom(pipeFrame,input)
importFrom(pipeFrame,loadConfig)
importFrom(pipeFrame,output)
importFrom(pipeFrame,processing)
importFrom(pipeFrame,regAttachedStep)
importFrom(pipeFrame,runWithFinishCheck)
importFrom(pipeFrame,saveConfig)
importFrom(pipeFrame,setGenome)
importFrom(pipeFrame,setJobName)
importFrom(pipeFrame,setPipeName)
importFrom(pipeFrame,setRefDir)
importFrom(pipeFrame,setThreads)
importFrom(pipeFrame,setTmpDir)
importFrom(pipeFrame,stepType)
importFrom(rJava,.jcall)
importFrom(rJava,.jnew)
importFrom(rJava,.jpackage)
importFrom(rhdf5,H5Fclose)
importFrom(rhdf5,H5Fopen)
importFrom(rhdf5,H5Gclose)
importFrom(rhdf5,H5Gopen)
importFrom(rhdf5,h5createFile)
importFrom(rhdf5,h5createGroup)
importFrom(rhdf5,h5write)
importFrom(rhdf5,h5writeAttribute)
importFrom(rmarkdown,render)
importFrom(rtracklayer,export)
importFrom(rtracklayer,export.bed)
importFrom(rtracklayer,export.bw)
importFrom(rtracklayer,export.wig)
importFrom(rtracklayer,import)
importFrom(rtracklayer,import.bed)
importFrom(stats,binom.test)
importFrom(stats,ecdf)
importFrom(stats,fft)
importFrom(stats,median)
importFrom(stats,runif)
importFrom(stringi,stri_split_fixed)
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,separate)
importFrom(tools,file_ext)
importFrom(tools,file_path_as_absolute)
importFrom(tools,md5sum)
importFrom(utils,download.file)
importFrom(utils,head)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,write.table)
importMethodsFrom(GenomicRanges,end)
importMethodsFrom(GenomicRanges,intersect)
importMethodsFrom(GenomicRanges,seqnames)
importMethodsFrom(GenomicRanges,start)
importMethodsFrom(GenomicRanges,strand)
importMethodsFrom(GenomicRanges,width)
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)
useDynLib(esATAC)