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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export("alphaThreshold<-")
export("baseMeanThreshold<-")
export("contrastName<-")
export("interestingGroups<-")
export("lfcShrink<-")
export("lfcThreshold<-")
export("resultsNames<-")
export(DESeqAnalysis)
export(DESeqAnalysisList)
export(DESeqResultsList)
export(alphaSummary)
export(alphaThreshold)
export(apeglmResults)
export(as.DESeqDataSet)
export(as.DESeqTransform)
export(baseMeanThreshold)
export(combine)
export(contrastName)
export(contrastSamples)
export(correlation)
export(deg)
export(degIntersection)
export(degPerContrast)
export(export)
export(importPairwiseContrasts)
export(interestingGroups)
export(lfcShrink)
export(lfcShrinkType)
export(lfcThreshold)
export(markdownTables)
export(plotBaseMean)
export(plotContrastScatter)
export(plotCorrelationHeatmap)
export(plotCounts)
export(plotDegHeatmap)
export(plotDegPca)
export(plotDegStackedBar)
export(plotDegUpset)
export(plotHeatmap)
export(plotLfc)
export(plotMa)
export(plotPca)
export(plotQuantileHeatmap)
export(plotVolcano)
export(prepareTximportFiles)
export(results)
export(resultsDiff)
export(resultsMatrix)
export(resultsNames)
export(resultsTables)
export(sampleData)
export(sanitizeTximportIdentifiers)
export(show)
export(transformType)
export(updateObject)
exportClasses(DESeqAnalysis)
exportClasses(DESeqAnalysisList)
exportClasses(DESeqResultsList)
exportMethods("[")
exportMethods("alphaThreshold<-")
exportMethods("baseMeanThreshold<-")
exportMethods("contrastName<-")
exportMethods("interestingGroups<-")
exportMethods("lfcShrink<-")
exportMethods("lfcThreshold<-")
exportMethods("resultsNames<-")
exportMethods(DESeqAnalysisList)
exportMethods(DESeqResultsList)
exportMethods(alphaSummary)
exportMethods(alphaThreshold)
exportMethods(apeglmResults)
exportMethods(as.DESeqDataSet)
exportMethods(as.DESeqTransform)
exportMethods(baseMeanThreshold)
exportMethods(coerce)
exportMethods(colnames)
exportMethods(combine)
exportMethods(contrastName)
exportMethods(contrastSamples)
exportMethods(correlation)
exportMethods(deg)
exportMethods(degIntersection)
exportMethods(degPerContrast)
exportMethods(dim)
exportMethods(dimnames)
exportMethods(export)
exportMethods(interestingGroups)
exportMethods(lfcShrink)
exportMethods(lfcShrinkType)
exportMethods(lfcThreshold)
exportMethods(markdownTables)
exportMethods(names)
exportMethods(plotBaseMean)
exportMethods(plotContrastScatter)
exportMethods(plotCorrelationHeatmap)
exportMethods(plotCounts)
exportMethods(plotDegHeatmap)
exportMethods(plotDegPca)
exportMethods(plotDegStackedBar)
exportMethods(plotDegUpset)
exportMethods(plotHeatmap)
exportMethods(plotLfc)
exportMethods(plotMa)
exportMethods(plotPca)
exportMethods(plotQuantileHeatmap)
exportMethods(plotVolcano)
exportMethods(results)
exportMethods(resultsDiff)
exportMethods(resultsMatrix)
exportMethods(resultsNames)
exportMethods(resultsTables)
exportMethods(rownames)
exportMethods(sampleData)
exportMethods(show)
exportMethods(transformType)
exportMethods(updateObject)
importClassesFrom(AcidBase,missingOrNULL)
importClassesFrom(AcidGenomes,TxToGene)
importClassesFrom(DESeq2,DESeqDataSet)
importClassesFrom(DESeq2,DESeqTransform)
importClassesFrom(IRanges,DFrameList)
importClassesFrom(SummarizedExperiment,RangedSummarizedExperiment)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(AcidBase,initDir)
importFrom(AcidBase,methodFunction)
importFrom(AcidBase,printString)
importFrom(AcidBase,realpath)
importFrom(AcidBase,showSlotInfo)
importFrom(AcidBase,standardizeCall)
importFrom(AcidBase,strMatch)
importFrom(AcidBase,tempdir2)
importFrom(AcidBase,unlink2)
importFrom(AcidCLI,abort)
importFrom(AcidCLI,alert)
importFrom(AcidCLI,alertInfo)
importFrom(AcidCLI,alertWarning)
importFrom(AcidCLI,dl)
importFrom(AcidCLI,toInlineString)
importFrom(AcidGenerics,"alphaThreshold<-")
importFrom(AcidGenerics,"baseMeanThreshold<-")
importFrom(AcidGenerics,"contrastName<-")
importFrom(AcidGenerics,"interestingGroups<-")
importFrom(AcidGenerics,"lfcShrink<-")
importFrom(AcidGenerics,"lfcThreshold<-")
importFrom(AcidGenerics,"metadata2<-")
importFrom(AcidGenerics,"resultsNames<-")
importFrom(AcidGenerics,GeneToSymbol)
importFrom(AcidGenerics,alphaSummary)
importFrom(AcidGenerics,alphaThreshold)
importFrom(AcidGenerics,as.DESeqDataSet)
importFrom(AcidGenerics,as.DESeqTransform)
importFrom(AcidGenerics,autopadZeros)
importFrom(AcidGenerics,baseMeanThreshold)
importFrom(AcidGenerics,camelCase)
importFrom(AcidGenerics,contrastName)
importFrom(AcidGenerics,contrastSamples)
importFrom(AcidGenerics,convertGenesToSymbols)
importFrom(AcidGenerics,convertSampleIdsToNames)
importFrom(AcidGenerics,correlation)
importFrom(AcidGenerics,deg)
importFrom(AcidGenerics,degIntersection)
importFrom(AcidGenerics,degPerContrast)
importFrom(AcidGenerics,droplevels2)
importFrom(AcidGenerics,export)
importFrom(AcidGenerics,import)
importFrom(AcidGenerics,interestingGroups)
importFrom(AcidGenerics,intersectionMatrix)
importFrom(AcidGenerics,leftJoin)
importFrom(AcidGenerics,lfcShrink)
importFrom(AcidGenerics,lfcShrinkType)
importFrom(AcidGenerics,lfcThreshold)
importFrom(AcidGenerics,makeNames)
importFrom(AcidGenerics,mapGenesToSymbols)
importFrom(AcidGenerics,markdownTables)
importFrom(AcidGenerics,melt)
importFrom(AcidGenerics,metadata2)
importFrom(AcidGenerics,plotBaseMean)
importFrom(AcidGenerics,plotContrastScatter)
importFrom(AcidGenerics,plotCorrelationHeatmap)
importFrom(AcidGenerics,plotCounts)
importFrom(AcidGenerics,plotDegHeatmap)
importFrom(AcidGenerics,plotDegPca)
importFrom(AcidGenerics,plotDegStackedBar)
importFrom(AcidGenerics,plotDegUpset)
importFrom(AcidGenerics,plotHeatmap)
importFrom(AcidGenerics,plotLfc)
importFrom(AcidGenerics,plotMa)
importFrom(AcidGenerics,plotPca)
importFrom(AcidGenerics,plotQuantileHeatmap)
importFrom(AcidGenerics,plotUpset)
importFrom(AcidGenerics,plotVolcano)
importFrom(AcidGenerics,removeNa)
importFrom(AcidGenerics,results)
importFrom(AcidGenerics,resultsDiff)
importFrom(AcidGenerics,resultsMatrix)
importFrom(AcidGenerics,resultsNames)
importFrom(AcidGenerics,resultsTables)
importFrom(AcidGenerics,sampleData)
importFrom(AcidGenerics,snakeCase)
importFrom(AcidGenerics,transformType)
importFrom(AcidMarkdown,markdownHeader)
importFrom(AcidMarkdown,markdownList)
importFrom(AcidPlots,.data)
importFrom(AcidPlots,acid_discrete_coord_flip)
importFrom(AcidPlots,acid_geom_label_repel)
importFrom(AcidPlots,acid_scale_color_discrete)
importFrom(AcidPlots,acid_scale_fill_discrete)
importFrom(AcidPlots,matchLabels)
importFrom(AcidPlots,pretty_breaks)
importFrom(AcidPlots,wrap_plots)
importFrom(BiocGenerics,Map)
importFrom(BiocGenerics,Reduce)
importFrom(BiocGenerics,anyDuplicated)
importFrom(BiocGenerics,as.data.frame)
importFrom(BiocGenerics,cbind)
importFrom(BiocGenerics,colnames)
importFrom(BiocGenerics,combine)
importFrom(BiocGenerics,counts)
importFrom(BiocGenerics,design)
importFrom(BiocGenerics,do.call)
importFrom(BiocGenerics,match)
importFrom(BiocGenerics,rownames)
importFrom(BiocGenerics,sort)
importFrom(BiocGenerics,unlist)
importFrom(BiocGenerics,updateObject)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,fpkm)
importFrom(DESeq2,nbinomWaldTest)
importFrom(DESeq2,priorInfo)
importFrom(IRanges,DataFrameList)
importFrom(IRanges,SplitDataFrameList)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,complete.cases)
importFrom(S4Vectors,cor)
importFrom(S4Vectors,decode)
importFrom(S4Vectors,droplevels)
importFrom(S4Vectors,head)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,na.omit)
importFrom(S4Vectors,split)
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(ggplot2,aes)
importFrom(ggplot2,after_stat)
importFrom(ggplot2,annotation_logticks)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_freqpoly)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,position_stack)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(goalie,allArePositive)
importFrom(goalie,areDisjointSets)
importFrom(goalie,areIntersectingSets)
importFrom(goalie,areSameLength)
importFrom(goalie,areSetEqual)
importFrom(goalie,assert)
importFrom(goalie,bapply)
importFrom(goalie,hasColnames)
importFrom(goalie,hasDuplicates)
importFrom(goalie,hasLength)
importFrom(goalie,hasNames)
importFrom(goalie,hasRownames)
importFrom(goalie,hasRows)
importFrom(goalie,hasValidDimnames)
importFrom(goalie,hasValidNames)
importFrom(goalie,isADir)
importFrom(goalie,isAFile)
importFrom(goalie,isAlpha)
importFrom(goalie,isAny)
importFrom(goalie,isCharacter)
importFrom(goalie,isFlag)
importFrom(goalie,isHeaderLevel)
importFrom(goalie,isInRange)
importFrom(goalie,isInt)
importFrom(goalie,isMatchingFixed)
importFrom(goalie,isNegative)
importFrom(goalie,isNonNegative)
importFrom(goalie,isNumber)
importFrom(goalie,isPercentage)
importFrom(goalie,isPositive)
importFrom(goalie,isScalar)
importFrom(goalie,isString)
importFrom(goalie,isSubset)
importFrom(goalie,isTximport)
importFrom(goalie,requireNamespaces)
importFrom(goalie,validate)
importFrom(methods,"slot<-")
importFrom(methods,.hasSlot)
importFrom(methods,as)
importFrom(methods,coerce)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,prototype)
importFrom(methods,setClass)
importFrom(methods,setGeneric)
importFrom(methods,setValidity)
importFrom(methods,show)
importFrom(methods,slot)
importFrom(methods,validObject)
importFrom(stats,model.matrix)
importFrom(stats,relevel)
importFrom(utils,capture.output)
importFrom(utils,getS3method)
importFrom(utils,packageName)
importFrom(utils,packageVersion)
importMethodsFrom(AcidBase,intersectionMatrix)
importMethodsFrom(AcidExperiment,"interestingGroups<-")
importMethodsFrom(AcidExperiment,GeneToSymbol)
importMethodsFrom(AcidExperiment,autopadZeros)
importMethodsFrom(AcidExperiment,convertGenesToSymbols)
importMethodsFrom(AcidExperiment,convertSampleIdsToNames)
importMethodsFrom(AcidExperiment,droplevels2)
importMethodsFrom(AcidExperiment,export)
importMethodsFrom(AcidExperiment,interestingGroups)
importMethodsFrom(AcidExperiment,mapGenesToSymbols)
importMethodsFrom(AcidExperiment,melt)
importMethodsFrom(AcidGenomes,GeneToSymbol)
importMethodsFrom(AcidPlots,plotCounts)
importMethodsFrom(AcidPlots,plotHeatmap)
importMethodsFrom(AcidPlots,plotPca)
importMethodsFrom(AcidPlots,plotUpset)
importMethodsFrom(AcidPlyr,leftJoin)
importMethodsFrom(AcidPlyr,melt)
importMethodsFrom(DESeq2,counts)
importMethodsFrom(DESeq2,design)
importMethodsFrom(pipette,"metadata2<-")
importMethodsFrom(pipette,droplevels2)
importMethodsFrom(pipette,export)
importMethodsFrom(pipette,import)
importMethodsFrom(pipette,metadata2)
importMethodsFrom(pipette,removeNa)
importMethodsFrom(syntactic,autopadZeros)
importMethodsFrom(syntactic,camelCase)
importMethodsFrom(syntactic,makeNames)
importMethodsFrom(syntactic,snakeCase)