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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(callCNV)
export(callLength)
export(callMetrics)
export(callMode)
export(callMotif)
export(callPeakDistance)
export(callSize)
export(callValleyDistance)
export(downsampleBam)
export(examplePath)
export(plotAllToOne)
export(plotCNV)
export(plotLength)
export(plotMetrics)
export(plotMode)
export(plotModeSummary)
export(plotMotif)
export(plotPeakDistance)
export(plotSingleGroup)
export(plotValleyDistance)
export(readBam)
export(readGALP)
export(read_bam_insert_metrics)
export(summariseBam)
export(summarizeBam)
import(Biostrings)
import(GenomeInfoDb)
import(GenomicAlignments)
import(Homo.sapiens)
import(QDNAseq)
import(Rsamtools)
import(S4Vectors)
import(dplyr)
import(ggplot2)
import(magrittr)
import(plyranges)
import(purrr)
import(stringr)
import(tibble)
import(tidyr)
importFrom(BSgenome,getSeq)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,unstrand)
importFrom(BiocGenerics,width)
importFrom(GenomeInfoDb,genome)
importFrom(GenomeInfoDb,isCircular)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicFeatures,genes)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,granges)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,seqnames)
importFrom(IRanges,IRanges)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,lag)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,summarize)
importFrom(dplyr,ungroup)
importFrom(ggrepel,geom_text_repel)
importFrom(magrittr,"%>%")
importFrom(plyranges,expand_ranges)
importFrom(plyranges,filter)
importFrom(plyranges,join_overlap_inner)
importFrom(purrr,map)
importFrom(quantmod,findValleys)
importFrom(rlang,.data)
importFrom(rlang,has_name)
importFrom(rtracklayer,export)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stringr,str_detect)
importFrom(tibble,tibble)
importFrom(utils,read.table)