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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export("counts<-")
export(alphaSummary)
export(as.DESeqDataSet)
export(as.DESeqTransform)
export(as.DGEList)
export(bcbioRNASeq)
export(bcbioRnaSeqTestsUrl)
export(camel)
export(counts)
export(loadRemoteData)
export(plot5Prime3PrimeBias)
export(plotCorrelationHeatmap)
export(plotCountDensity)
export(plotCounts)
export(plotCountsPerBiotype)
export(plotCountsPerBroadClass)
export(plotCountsPerFeature)
export(plotCountsPerGene)
export(plotDEGHeatmap)
export(plotDegHeatmap)
export(plotDispEsts)
export(plotExonicMappingRate)
export(plotFeatureSaturation)
export(plotFeaturesDetected)
export(plotGenderMarkers)
export(plotGeneSaturation)
export(plotGenesDetected)
export(plotHeatmap)
export(plotIntronicMappingRate)
export(plotMA)
export(plotMappedReads)
export(plotMappingRate)
export(plotMeanAverage)
export(plotMeanSD)
export(plotMeanSd)
export(plotPCA)
export(plotPCACovariates)
export(plotPca)
export(plotPcaCovariates)
export(plotPseudoVsAlignedCounts)
export(plotQC)
export(plotQc)
export(plotQuantileHeatmap)
export(plotRRNAMappingRate)
export(plotRrnaMappingRate)
export(plotTotalReads)
export(prepareRNASeqTemplate)
export(relativeLogExpression)
export(saveData)
export(show)
export(slotAlignedCounts)
export(tmm)
export(topTables)
export(updateObject)
export(writeCounts)
exportClasses(bcbioRNASeq)
exportMethods("[")
exportMethods(as.DESeqDataSet)
exportMethods(as.DESeqTransform)
exportMethods(as.DGEList)
exportMethods(coerce)
exportMethods(counts)
exportMethods(plot5Prime3PrimeBias)
exportMethods(plotCorrelationHeatmap)
exportMethods(plotCounts)
exportMethods(plotCountsPerBiotype)
exportMethods(plotCountsPerBroadClass)
exportMethods(plotCountsPerFeature)
exportMethods(plotDegHeatmap)
exportMethods(plotDispEsts)
exportMethods(plotExonicMappingRate)
exportMethods(plotFeatureSaturation)
exportMethods(plotGenderMarkers)
exportMethods(plotIntronicMappingRate)
exportMethods(plotMappedReads)
exportMethods(plotMappingRate)
exportMethods(plotMeanSd)
exportMethods(plotPca)
exportMethods(plotPcaCovariates)
exportMethods(plotPseudoVsAlignedCounts)
exportMethods(plotQc)
exportMethods(plotRrnaMappingRate)
exportMethods(plotTotalReads)
exportMethods(relativeLogExpression)
exportMethods(show)
exportMethods(slotAlignedCounts)
exportMethods(tmm)
exportMethods(updateObject)
importClassesFrom(AcidGenomes,TxToGene)
importClassesFrom(DESeq2,DESeqDataSet)
importClassesFrom(DESeq2,DESeqTransform)
importClassesFrom(IRanges,DFrameList)
importClassesFrom(SummarizedExperiment,RangedSummarizedExperiment)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importClassesFrom(edgeR,DGEList)
importFrom(AcidBase,dots)
importFrom(AcidBase,methodFormals)
importFrom(AcidBase,realpath)
importFrom(AcidBase,showSlotInfo)
importFrom(AcidBase,standardizeCall)
importFrom(AcidCLI,abort)
importFrom(AcidCLI,alert)
importFrom(AcidCLI,alertInfo)
importFrom(AcidCLI,alertSuccess)
importFrom(AcidCLI,alertWarning)
importFrom(AcidCLI,dl)
importFrom(AcidCLI,h1)
importFrom(AcidCLI,h2)
importFrom(AcidCLI,h3)
importFrom(AcidCLI,toInlineString)
importFrom(AcidCLI,txt)
importFrom(AcidCLI,ul)
importFrom(AcidExperiment,detectLanes)
importFrom(AcidExperiment,importSampleData)
importFrom(AcidExperiment,makeSummarizedExperiment)
importFrom(AcidExperiment,matchInterestingGroups)
importFrom(AcidGenerics,"interestingGroups<-")
importFrom(AcidGenerics,alphaSummary)
importFrom(AcidGenerics,as.DESeqDataSet)
importFrom(AcidGenerics,as.DESeqTransform)
importFrom(AcidGenerics,as.DGEList)
importFrom(AcidGenerics,camelCase)
importFrom(AcidGenerics,droplevels2)
importFrom(AcidGenerics,encode)
importFrom(AcidGenerics,humanize)
importFrom(AcidGenerics,interestingGroups)
importFrom(AcidGenerics,makeNames)
importFrom(AcidGenerics,mapGenesToRownames)
importFrom(AcidGenerics,markdownTables)
importFrom(AcidGenerics,metrics)
importFrom(AcidGenerics,plot5Prime3PrimeBias)
importFrom(AcidGenerics,plotCorrelationHeatmap)
importFrom(AcidGenerics,plotCounts)
importFrom(AcidGenerics,plotCountsCorrelation)
importFrom(AcidGenerics,plotCountsCorrelationHeatmap)
importFrom(AcidGenerics,plotCountsPerBiotype)
importFrom(AcidGenerics,plotCountsPerBroadClass)
importFrom(AcidGenerics,plotCountsPerFeature)
importFrom(AcidGenerics,plotDegHeatmap)
importFrom(AcidGenerics,plotExonicMappingRate)
importFrom(AcidGenerics,plotFeatureSaturation)
importFrom(AcidGenerics,plotFeaturesDetected)
importFrom(AcidGenerics,plotGenderMarkers)
importFrom(AcidGenerics,plotHeatmap)
importFrom(AcidGenerics,plotIntronicMappingRate)
importFrom(AcidGenerics,plotMappedReads)
importFrom(AcidGenerics,plotMappingRate)
importFrom(AcidGenerics,plotMeanSd)
importFrom(AcidGenerics,plotPca)
importFrom(AcidGenerics,plotPcaCovariates)
importFrom(AcidGenerics,plotPseudoVsAlignedCounts)
importFrom(AcidGenerics,plotQc)
importFrom(AcidGenerics,plotQuantileHeatmap)
importFrom(AcidGenerics,plotRrnaMappingRate)
importFrom(AcidGenerics,plotTotalReads)
importFrom(AcidGenerics,relativeLogExpression)
importFrom(AcidGenerics,sampleData)
importFrom(AcidGenerics,showHeader)
importFrom(AcidGenerics,slotAlignedCounts)
importFrom(AcidGenerics,stripTranscriptVersions)
importFrom(AcidGenerics,tmm)
importFrom(AcidGenomes,TxToGene)
importFrom(AcidGenomes,detectOrganism)
importFrom(AcidGenomes,emptyRanges)
importFrom(AcidGenomes,importTxToGene)
importFrom(AcidGenomes,makeGRangesFromEnsembl)
importFrom(AcidGenomes,makeGRangesFromGff)
importFrom(AcidPlots,.data)
importFrom(AcidPlots,acid_discrete_coord_flip)
importFrom(AcidPlots,acid_geom_abline)
importFrom(AcidPlots,acid_geom_bar)
importFrom(AcidPlots,acid_geom_label_repel)
importFrom(AcidPlots,acid_scale_color_discrete)
importFrom(AcidPlots,acid_scale_fill_discrete)
importFrom(AcidPlots,acid_scale_y_continuous_nopad)
importFrom(AcidPlots,matchLabels)
importFrom(AcidPlots,pretty_breaks)
importFrom(AcidPlots,wrap_plots)
importFrom(BiocGenerics,"counts<-")
importFrom(BiocGenerics,as.data.frame)
importFrom(BiocGenerics,counts)
importFrom(BiocGenerics,do.call)
importFrom(BiocGenerics,estimateSizeFactors)
importFrom(BiocGenerics,plotDispEsts)
importFrom(BiocGenerics,updateObject)
importFrom(BiocGenerics,width)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSet)
importFrom(DESeq2,fpkm)
importFrom(DESeq2,rlog)
importFrom(DESeq2,varianceStabilizingTransformation)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,cbind)
importFrom(S4Vectors,droplevels)
importFrom(S4Vectors,getListElement)
importFrom(S4Vectors,head)
importFrom(S4Vectors,lapply)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assayNames<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(bcbioBase,getGtfFileFromYaml)
importFrom(bcbioBase,getMetricsFromYaml)
importFrom(bcbioBase,getSampleDataFromYaml)
importFrom(bcbioBase,importDataVersions)
importFrom(bcbioBase,importProgramVersions)
importFrom(bcbioBase,projectDir)
importFrom(bcbioBase,runDate)
importFrom(bcbioBase,sampleDirs)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,cpm)
importFrom(edgeR,scaleOffset)
importFrom(ggplot2,aes)
importFrom(ggplot2,expand_limits)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(goalie,allAreMatchingFixed)
importFrom(goalie,areDisjointSets)
importFrom(goalie,areIntersectingSets)
importFrom(goalie,areSetEqual)
importFrom(goalie,assert)
importFrom(goalie,bapply)
importFrom(goalie,hasDimnames)
importFrom(goalie,hasLength)
importFrom(goalie,hasUniqueCols)
importFrom(goalie,hasValidDimnames)
importFrom(goalie,isADir)
importFrom(goalie,isAFile)
importFrom(goalie,isAUrl)
importFrom(goalie,isAny)
importFrom(goalie,isCharacter)
importFrom(goalie,isDir)
importFrom(goalie,isFile)
importFrom(goalie,isFlag)
importFrom(goalie,isGgscale)
importFrom(goalie,isInRange)
importFrom(goalie,isInt)
importFrom(goalie,isNonNegative)
importFrom(goalie,isNumber)
importFrom(goalie,isPositive)
importFrom(goalie,isProportion)
importFrom(goalie,isString)
importFrom(goalie,isSubset)
importFrom(goalie,isTximport)
importFrom(goalie,requireNamespaces)
importFrom(goalie,validNames)
importFrom(goalie,validate)
importFrom(goalie,validateClasses)
importFrom(methods,"as<-")
importFrom(methods,"slot<-")
importFrom(methods,.hasSlot)
importFrom(methods,as)
importFrom(methods,coerce)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setAs)
importFrom(methods,setClass)
importFrom(methods,setMethod)
importFrom(methods,setValidity)
importFrom(methods,show)
importFrom(methods,slot)
importFrom(methods,validObject)
importFrom(pipette,export)
importFrom(pipette,import)
importFrom(pipette,loadRemoteData)
importFrom(pipette,saveData)
importFrom(tximport,tximport)
importFrom(utils,capture.output)
importFrom(utils,packageName)
importFrom(utils,packageVersion)
importFrom(utils,sessionInfo)
importMethodsFrom(AcidBase,showHeader)
importMethodsFrom(AcidExperiment,"interestingGroups<-")
importMethodsFrom(AcidExperiment,droplevels2)
importMethodsFrom(AcidExperiment,humanize)
importMethodsFrom(AcidExperiment,interestingGroups)
importMethodsFrom(AcidExperiment,mapGenesToRownames)
importMethodsFrom(AcidExperiment,metrics)
importMethodsFrom(AcidExperiment,sampleData)
importMethodsFrom(AcidExperiment,stripTranscriptVersions)
importMethodsFrom(AcidGenomes,stripTranscriptVersions)
importMethodsFrom(AcidPlots,plotCorrelationHeatmap)
importMethodsFrom(AcidPlots,plotCountsCorrelation)
importMethodsFrom(AcidPlots,plotCountsCorrelationHeatmap)
importMethodsFrom(AcidPlots,plotCountsPerBiotype)
importMethodsFrom(AcidPlots,plotCountsPerBroadClass)
importMethodsFrom(AcidPlots,plotCountsPerFeature)
importMethodsFrom(AcidPlots,plotFeaturesDetected)
importMethodsFrom(AcidPlots,plotGenderMarkers)
importMethodsFrom(AcidPlots,plotHeatmap)
importMethodsFrom(AcidPlots,plotPca)
importMethodsFrom(AcidPlots,plotQuantileHeatmap)
importMethodsFrom(DESeq2,estimateSizeFactors)
importMethodsFrom(pipette,droplevels2)
importMethodsFrom(pipette,encode)
importMethodsFrom(pipette,export)
importMethodsFrom(pipette,import)
importMethodsFrom(syntactic,camelCase)
importMethodsFrom(syntactic,makeNames)