# Generated by roxygen2: do not edit by hand

export(addOffsets)
export(callPatterns)
export(callPeaks)
export(cleanCounts)
export(controlEM)
export(epigraHMM)
export(epigraHMMDataSetFromBam)
export(epigraHMMDataSetFromMatrix)
export(estimateTransitionProb)
export(expStep)
export(info)
export(initializer)
export(maxStepProb)
export(normalizeCounts)
export(plotCounts)
export(plotPatterns)
export(segmentGenome)
export(simulateMarkovChain)
import(GreyListChIP)
import(Rhdf5lib)
import(data.table)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,tile)
importFrom(GenomicRanges,tileGenome)
importFrom(GenomicRanges,width)
importFrom(IRanges,overlapsAny)
importFrom(IRanges,union)
importFrom(MASS,glm.nb)
importFrom(Matrix,Matrix)
importFrom(Rcpp,sourceCpp)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,scanBam)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,decode)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,subjectHits)
importFrom(Seqinfo,Seqinfo)
importFrom(Seqinfo,genome)
importFrom(Seqinfo,seqnames)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(SummarizedExperiment,seqnames)
importFrom(bamsignals,bamCount)
importFrom(csaw,correlateReads)
importFrom(csaw,maximizeCcf)
importFrom(csaw,readParam)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_area)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_path)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggpubr,ggarrange)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,palette.colors)
importFrom(limma,loessFit)
importFrom(magrittr,"%>%")
importFrom(methods,is)
importFrom(pheatmap,pheatmap)
importFrom(rhdf5,h5read)
importFrom(rtracklayer,BEDFile)
importFrom(rtracklayer,browserSession)
importFrom(rtracklayer,getTable)
importFrom(rtracklayer,import)
importFrom(rtracklayer,ucscTableQuery)
importFrom(rtracklayer,wigToBigWig)
importFrom(scales,comma)
importFrom(stats,predict)
importFrom(stats,quantile)
useDynLib(epigraHMM, .registration = TRUE)
