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# Generated by roxygen2: do not edit by hand
export(addGCBintoMethylome)
export(computeDeviation)
export(computeZScoreVariability)
export(deviationZScores)
export(deviations)
export(differential_deviation_test)
export(plotExpectedFootprint)
export(plotMotifFootprint)
export(read_methylome)
export(run_methylTFR_RnBeads)
export(run_methyltfr)
exportClasses(methylTFRdeviations)
exportMethods(cbind)
exportMethods(deviationZScores)
exportMethods(deviations)
exportMethods(rbind)
import(R.utils)
import(data.table)
import(logger)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(BiocGenerics,cbind)
importFrom(BiocGenerics,rbind)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,SnowParam)
importFrom(BiocParallel,bplapply)
importFrom(DelayedArray,ArbitraryArrayGrid)
importFrom(DelayedArray,DelayedArray)
importFrom(DelayedArray,close)
importFrom(DelayedArray,write_block)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,width)
importFrom(HDF5Array,HDF5RealizationSink)
importFrom(IRanges,IRanges)
importFrom(IRanges,subsetByOverlaps)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,mcols)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(data.table,":=")
importFrom(data.table,.N)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,setDT)
importFrom(ggplot2,aes)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(logger,log_error)
importFrom(logger,log_info)
importFrom(logger,log_success)
importFrom(logger,log_warn)
importFrom(matrixStats,colMads)
importFrom(matrixStats,colMeans2)
importFrom(matrixStats,colMedians)
importFrom(matrixStats,colSds)
importFrom(matrixStats,rowMeans2)
importFrom(matrixStats,rowSds)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setMethod)
importFrom(stats,aggregate)
importFrom(stats,aov)
importFrom(stats,kruskal.test)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stats,t.test)
importFrom(stats,wilcox.test)
importFrom(stringr,str_replace)
importFrom(stringr,str_split)
importFrom(utils,read.table)