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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(ChrawExperimentFromDataFrame)
export(ChrawExperimentFromSampleFile)
export(addCountExperiment)
export(addFragmentLengthDist)
export(addRNASeqExperiment)
export(annotateExperimentRegions)
export(assignPeaks2GeneDE)
export(assignPeaks2Peaks)
export(calculateMetaProfiles)
export(computeFragLengthDist)
export(enrichAnno)
export(getDiffResultSummary)
export(getGenomicBins)
export(importAndAverage)
export(importNarrowPeaks)
export(importNarrowPeaksFromFile)
export(plotChrMStats)
export(plotCovFromDF)
export(plotDiffScatter)
export(plotEnrichResults)
export(plotFracReadsInAnnot)
export(plotFragmentLengthDist)
export(plotFripStats)
export(plotMappingStats)
export(plotMetaProfileHeatmaps)
export(plotPCRDuplicateStats)
export(plotSampleCorrelations)
export(plotVProfile)
export(plotVolcano)
export(pullDiffResults)
export(reformatMatrixScores)
export(rewrite_paths)
export(selectBSgenome)
export(selectChromHMMData)
export(selectOrgDb)
export(selectTxDb)
export(testForDiffSignal)
export(tidyChrawExperiment)
exportClasses(ChrawExperiment)
exportMethods(c)
exportMethods(getGenomicBins)
exportMethods(indexBam)
exportMethods(plotMA)
exportMethods(plotPCA)
exportMethods(plotVolcano)
import(BiocParallel)
import(GenomicRanges)
import(MultiAssayExperiment)
import(Rsamtools)
import(cowplot)
import(ggplot2)
import(rlang)
importClassesFrom(AnnotationDbi,OrgDb)
importClassesFrom(BSgenome,BSgenome)
importClassesFrom(GenomicFeatures,TxDb)
importClassesFrom(IRanges,CompressedCharacterList)
importClassesFrom(MultiAssayExperiment,MultiAssayExperiment)
importFrom(BiocGenerics,plotMA)
importFrom(BiocParallel,bplapply)
importFrom(ChIPpeakAnno,annotatePeakInBatch)
importFrom(ChIPseeker,annotatePeak)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,anno_lines)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,estimateSizeFactorsForMatrix)
importFrom(DESeq2,results)
importFrom(GenomicAlignments,first)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(GenomicAlignments,second)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(Rsubread,featureCounts)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(circlize,colorRamp2)
importFrom(csaw,getPESizes)
importFrom(ensembldb,select)
importFrom(genomation,ScoreMatrixList)
importFrom(jsonlite,fromJSON)
importFrom(magrittr,"%>%")
importFrom(matrixStats,rowVars)
importFrom(random,randomStrings)
importFrom(rtracklayer,import)
importFrom(txdbmaker,makeTxDbFromGFF)
importMethodsFrom(BiocGenerics,mean)
importMethodsFrom(BiocGenerics,plotPCA)
importMethodsFrom(Rsamtools,indexBam)
importMethodsFrom(S4Vectors,"%in%")
importMethodsFrom(S4Vectors,elementMetadata)