# Generated by roxygen2: do not edit by hand

export("counts<-")
export(alphaSummary)
export(bcbioRNASeq)
export(bcbioRNASeqTestsURL)
export(contrastName)
export(counts)
export(loadRNASeq)
export(plot5Prime3PrimeBias)
export(plotCorrelationHeatmap)
export(plotCountDensity)
export(plotCounts)
export(plotCountsPerBiotype)
export(plotCountsPerBroadClass)
export(plotCountsPerFeature)
export(plotCountsPerGene)
export(plotDEGHeatmap)
export(plotDEGPCA)
export(plotDispEsts)
export(plotExonicMappingRate)
export(plotFeaturesDetected)
export(plotGenderMarkers)
export(plotGeneSaturation)
export(plotGenesDetected)
export(plotHeatmap)
export(plotIntronicMappingRate)
export(plotMA)
export(plotMappedReads)
export(plotMappingRate)
export(plotMeanAverage)
export(plotMeanSD)
export(plotPCA)
export(plotPCACovariates)
export(plotPseudoVsAlignedCounts)
export(plotQC)
export(plotQuantileHeatmap)
export(plotRRNAMappingRate)
export(plotTotalReads)
export(plotVolcano)
export(prepareRNASeqTemplate)
export(relativeLogExpression)
export(resultsTables)
export(slotAlignedCounts)
export(tmm)
export(topTables)
exportClasses(bcbioRNASeq)
exportMethods("[")
exportMethods(coerce)
exportMethods(counts)
exportMethods(plot5Prime3PrimeBias)
exportMethods(plotCorrelationHeatmap)
exportMethods(plotCounts)
exportMethods(plotCountsPerBiotype)
exportMethods(plotCountsPerBroadClass)
exportMethods(plotCountsPerFeature)
exportMethods(plotDispEsts)
exportMethods(plotExonicMappingRate)
exportMethods(plotGenderMarkers)
exportMethods(plotGeneSaturation)
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(DESeq2,DESeqDataSet)
importClassesFrom(DESeq2,DESeqTransform)
importClassesFrom(SummarizedExperiment,RangedSummarizedExperiment)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importClassesFrom(basejump,Tx2Gene)
importClassesFrom(edgeR,DGEList)
importFrom(BiocGenerics,"counts<-")
importFrom(BiocGenerics,colSums)
importFrom(BiocGenerics,counts)
importFrom(BiocGenerics,plotDispEsts)
importFrom(BiocGenerics,plotPCA)
importFrom(BiocGenerics,rowSums)
importFrom(BiocGenerics,updateObject)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSet)
importFrom(DESeq2,estimateSizeFactors)
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,as.data.frame)
importFrom(S4Vectors,cbind)
importFrom(S4Vectors,do.call)
importFrom(S4Vectors,getListElement)
importFrom(S4Vectors,head)
importFrom(S4Vectors,lapply)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,sapply)
importFrom(S4Vectors,width)
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(acidplots,acid_coord_flip)
importFrom(acidplots,acid_geom_abline)
importFrom(acidplots,acid_geom_bar)
importFrom(acidplots,acid_geom_label_repel)
importFrom(acidplots,acid_scale_y_continuous_nopad)
importFrom(acidplots,matchLabels)
importFrom(acidplots,plotCountsCorrelation)
importFrom(acidplots,plotCountsCorrelationHeatmap)
importFrom(acidplots,plotFeaturesDetected)
importFrom(acidplots,plotHeatmap)
importFrom(acidplots,plotQuantileHeatmap)
importFrom(basejump,"interestingGroups<-")
importFrom(basejump,Tx2Gene)
importFrom(basejump,camelCase)
importFrom(basejump,detectLanes)
importFrom(basejump,detectOrganism)
importFrom(basejump,droplevels)
importFrom(basejump,emptyRanges)
importFrom(basejump,encode)
importFrom(basejump,formalsList)
importFrom(basejump,humanize)
importFrom(basejump,import)
importFrom(basejump,importSampleData)
importFrom(basejump,importTx2Gene)
importFrom(basejump,interestingGroups)
importFrom(basejump,makeGRangesFromEnsembl)
importFrom(basejump,makeGRangesFromGFF)
importFrom(basejump,makeNames)
importFrom(basejump,makeSummarizedExperiment)
importFrom(basejump,mapGenesToRownames)
importFrom(basejump,matchArgsToDoCall)
importFrom(basejump,matchInterestingGroups)
importFrom(basejump,methodFormals)
importFrom(basejump,metrics)
importFrom(basejump,realpath)
importFrom(basejump,sampleData)
importFrom(basejump,showSlotInfo)
importFrom(basejump,standardizeCall)
importFrom(basejump,stripTranscriptVersions)
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(bioverbs,plot5Prime3PrimeBias)
importFrom(bioverbs,plotCorrelationHeatmap)
importFrom(bioverbs,plotCounts)
importFrom(bioverbs,plotCountsPerBiotype)
importFrom(bioverbs,plotCountsPerBroadClass)
importFrom(bioverbs,plotCountsPerFeature)
importFrom(bioverbs,plotExonicMappingRate)
importFrom(bioverbs,plotGenderMarkers)
importFrom(bioverbs,plotGeneSaturation)
importFrom(bioverbs,plotIntronicMappingRate)
importFrom(bioverbs,plotMappedReads)
importFrom(bioverbs,plotMappingRate)
importFrom(bioverbs,plotMeanSD)
importFrom(bioverbs,plotPCACovariates)
importFrom(bioverbs,plotQC)
importFrom(bioverbs,plotRRNAMappingRate)
importFrom(bioverbs,plotTotalReads)
importFrom(bioverbs,relativeLogExpression)
importFrom(bioverbs,tmm)
importFrom(cowplot,plot_grid)
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,areDisjointSets)
importFrom(goalie,areIntersectingSets)
importFrom(goalie,areSetEqual)
importFrom(goalie,assert)
importFrom(goalie,bapply)
importFrom(goalie,containsAURL)
importFrom(goalie,hasDimnames)
importFrom(goalie,hasLength)
importFrom(goalie,hasUniqueCols)
importFrom(goalie,hasValidDimnames)
importFrom(goalie,isADirectory)
importFrom(goalie,isAFile)
importFrom(goalie,isAny)
importFrom(goalie,isCharacter)
importFrom(goalie,isDirectory)
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,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(rlang,"!!")
importFrom(rlang,sym)
importFrom(scales,pretty_breaks)
importFrom(sessioninfo,session_info)
importFrom(tximport,tximport)
importFrom(utils,capture.output)
importFrom(utils,globalVariables)
importFrom(utils,packageVersion)
importMethodsFrom(acidplots,plotCorrelationHeatmap)
importMethodsFrom(acidplots,plotCounts)
importMethodsFrom(acidplots,plotCountsPerBiotype)
importMethodsFrom(acidplots,plotCountsPerBroadClass)
importMethodsFrom(acidplots,plotCountsPerFeature)
importMethodsFrom(acidplots,plotGenderMarkers)
importMethodsFrom(acidplots,plotPCA)
importMethodsFrom(basejump,coerce)
