# Generated by roxygen2: do not edit by hand

export(GUIDEseqAnalysis)
export(PEtagAnalysis)
export(annotateOffTargets)
export(buildFeatureVectorForScoringBulge)
export(combineOfftargets)
export(createBarcodeFasta)
export(getBestAlnInfo)
export(getPeaks)
export(getUniqueCleavageEvents)
export(getUsedBarcodes)
export(mergePlusMinusPeaks)
export(offTargetAnalysisOfPeakRegions)
export(offTargetAnalysisWithBulge)
export(plotAlignedOfftargets)
export(plotTracks)
import(BSgenome, except=export)
import(BiocGenerics, except=c(var, sd))
import(GenomicRanges, except=values)
import(IRanges, except=values)
import(S4Vectors, except=c(fold, values, rename))
import(patchwork)
importFrom(BSgenome,getSeq)
importFrom(BiocGenerics,cbind)
importFrom(BiocGenerics,grep)
importFrom(BiocGenerics,lapply)
importFrom(BiocGenerics,rbind)
importFrom(BiocGenerics,relist)
importFrom(BiocGenerics,rep.int)
importFrom(BiocGenerics,sort)
importFrom(BiocGenerics,subset)
importFrom(BiocGenerics,toTable)
importFrom(BiocGenerics,unlist)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,alignedPattern)
importFrom(Biostrings,alignedSubject)
importFrom(Biostrings,complement)
importFrom(Biostrings,extractAt)
importFrom(Biostrings,isMatchingAt)
importFrom(Biostrings,neditAt)
importFrom(Biostrings,nucleotideSubstitutionMatrix)
importFrom(Biostrings,pairwiseAlignment)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,replaceAt)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,score)
importFrom(Biostrings,start)
importFrom(Biostrings,subject)
importFrom(Biostrings,substring)
importFrom(Biostrings,width)
importFrom(CRISPRseek,compare2Sequences)
importFrom(ChIPpeakAnno,annotatePeakInBatch)
importFrom(GenomeInfoDb,"seqinfo<-")
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,"seqlevelsStyle<-")
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicAlignments,first)
importFrom(GenomicAlignments,last)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(GenomicAlignments,readGAlignmentsList)
importFrom(GenomicFeatures,exons)
importFrom(GenomicFeatures,genes)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,score)
importFrom(GenomicRanges,seqinfo)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,strand)
importFrom(IRanges,IRanges)
importFrom(IRanges,IRangesList)
importFrom(IRanges,PartitioningByEnd)
importFrom(IRanges,Views)
importFrom(IRanges,coverage)
importFrom(IRanges,nearest)
importFrom(IRanges,overlapsAny)
importFrom(IRanges,ranges)
importFrom(IRanges,runLength)
importFrom(IRanges,runsum)
importFrom(IRanges,viewWhichMaxs)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,bamFlagTest)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,elementNROWS)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,orderIntegerPairs)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,runValue)
importFrom(S4Vectors,subjectHits)
importFrom(S4Vectors,unstrsplit)
importFrom(data.table,fread)
importFrom(dplyr,'%>%')
importFrom(dplyr,add_count)
importFrom(dplyr,arrange)
importFrom(dplyr,count)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,slice_sample)
importFrom(dplyr,summarize)
importFrom(dplyr,top_n)
importFrom(dplyr,ungroup)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_gradient)
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(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,hist)
importFrom(graphics,par)
importFrom(hash,hash)
importFrom(hash,values)
importFrom(limma,vennCounts)
importFrom(limma,vennDiagram)
importFrom(matrixStats,rowMaxs)
importFrom(matrixStats,rowMins)
importFrom(methods,as)
importFrom(methods,is)
importFrom(multtest,mt.rawp2adjp)
importFrom(openxlsx,addWorksheet)
importFrom(openxlsx,createStyle)
importFrom(openxlsx,createWorkbook)
importFrom(openxlsx,saveWorkbook)
importFrom(openxlsx,writeData)
importFrom(parallel,clusterExport)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,parLapply)
importFrom(parallel,stopCluster)
importFrom(purrr,map)
importFrom(rio,import)
importFrom(rlang,sym)
importFrom(stats,fisher.test)
importFrom(stats,p.adjust)
importFrom(stats,pnbinom)
importFrom(stats,ppois)
importFrom(stats,setNames)
importFrom(stringr,str_c)
importFrom(tidyr,unnest)
importFrom(tools,file_ext)
importFrom(utils,read.table)
importFrom(utils,write.table)
