# Generated by roxygen2: do not edit by hand

export("alphaThreshold<-")
export("baseMeanThreshold<-")
export("contrastName<-")
export("contrastNames<-")
export("interestingGroups<-")
export("lfcShrink<-")
export("lfcThreshold<-")
export("resultsNames<-")
export(DESeqAnalysis)
export(DESeqAnalysisList)
export(alphaSummary)
export(alphaThreshold)
export(apeglmContrast)
export(apeglmResults)
export(baseMeanThreshold)
export(combine)
export(contrastName)
export(contrastNames)
export(contrastSamples)
export(correlation)
export(deg)
export(degIntersection)
export(degPerContrast)
export(export)
export(importPairwiseContrasts)
export(interestingGroups)
export(lfcShrink)
export(lfcShrinkType)
export(lfcThreshold)
export(markdown)
export(matchMetadataToFiles)
export(plotBaseMean)
export(plotCorrelationHeatmap)
export(plotCounts)
export(plotDEGHeatmap)
export(plotDEGPCA)
export(plotDEGStackedBar)
export(plotDEGUpset)
export(plotHeatmap)
export(plotMA)
export(plotMeanAverage)
export(plotPCA)
export(plotQuantileHeatmap)
export(plotVolcano)
export(prepareTximportFiles)
export(results)
export(resultsDiff)
export(resultsMatrix)
export(resultsNames)
export(resultsTables)
export(sampleData)
export(topTables)
export(transformType)
exportClasses(DESeqAnalysis)
exportClasses(DESeqAnalysisList)
exportMethods("alphaThreshold<-")
exportMethods("baseMeanThreshold<-")
exportMethods("contrastName<-")
exportMethods("contrastNames<-")
exportMethods("interestingGroups<-")
exportMethods("lfcShrink<-")
exportMethods("lfcThreshold<-")
exportMethods("resultsNames<-")
exportMethods(alphaSummary)
exportMethods(alphaThreshold)
exportMethods(apeglmResults)
exportMethods(baseMeanThreshold)
exportMethods(coerce)
exportMethods(combine)
exportMethods(contrastName)
exportMethods(contrastNames)
exportMethods(contrastSamples)
exportMethods(correlation)
exportMethods(deg)
exportMethods(degIntersection)
exportMethods(degPerContrast)
exportMethods(export)
exportMethods(interestingGroups)
exportMethods(lfcShrink)
exportMethods(lfcShrinkType)
exportMethods(lfcThreshold)
exportMethods(markdown)
exportMethods(plotBaseMean)
exportMethods(plotCorrelationHeatmap)
exportMethods(plotCounts)
exportMethods(plotDEGHeatmap)
exportMethods(plotDEGPCA)
exportMethods(plotDEGStackedBar)
exportMethods(plotDEGUpset)
exportMethods(plotHeatmap)
exportMethods(plotMA)
exportMethods(plotPCA)
exportMethods(plotQuantileHeatmap)
exportMethods(plotVolcano)
exportMethods(results)
exportMethods(resultsDiff)
exportMethods(resultsMatrix)
exportMethods(resultsNames)
exportMethods(resultsTables)
exportMethods(sampleData)
exportMethods(show)
exportMethods(topTables)
exportMethods(transformType)
exportMethods(updateObject)
importClassesFrom(DESeq2,DESeqDataSet)
importClassesFrom(DESeq2,DESeqTransform)
importClassesFrom(SummarizedExperiment,RangedSummarizedExperiment)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importClassesFrom(basejump,Tx2Gene)
importFrom(AcidGenerics,"alphaThreshold<-")
importFrom(AcidGenerics,"baseMeanThreshold<-")
importFrom(AcidGenerics,"contrastName<-")
importFrom(AcidGenerics,"contrastNames<-")
importFrom(AcidGenerics,"lfcShrink<-")
importFrom(AcidGenerics,"lfcThreshold<-")
importFrom(AcidGenerics,"resultsNames<-")
importFrom(AcidGenerics,alphaSummary)
importFrom(AcidGenerics,alphaThreshold)
importFrom(AcidGenerics,baseMeanThreshold)
importFrom(AcidGenerics,contrastName)
importFrom(AcidGenerics,contrastNames)
importFrom(AcidGenerics,contrastSamples)
importFrom(AcidGenerics,deg)
importFrom(AcidGenerics,degIntersection)
importFrom(AcidGenerics,degPerContrast)
importFrom(AcidGenerics,export)
importFrom(AcidGenerics,lfcShrink)
importFrom(AcidGenerics,lfcShrinkType)
importFrom(AcidGenerics,lfcThreshold)
importFrom(AcidGenerics,markdown)
importFrom(AcidGenerics,plotBaseMean)
importFrom(AcidGenerics,plotCorrelationHeatmap)
importFrom(AcidGenerics,plotCounts)
importFrom(AcidGenerics,plotDEGHeatmap)
importFrom(AcidGenerics,plotDEGPCA)
importFrom(AcidGenerics,plotDEGStackedBar)
importFrom(AcidGenerics,plotDEGUpset)
importFrom(AcidGenerics,plotHeatmap)
importFrom(AcidGenerics,plotQuantileHeatmap)
importFrom(AcidGenerics,plotVolcano)
importFrom(AcidGenerics,results)
importFrom(AcidGenerics,resultsDiff)
importFrom(AcidGenerics,resultsMatrix)
importFrom(AcidGenerics,resultsNames)
importFrom(AcidGenerics,resultsTables)
importFrom(AcidGenerics,sampleData)
importFrom(AcidGenerics,topTables)
importFrom(AcidGenerics,transformType)
importFrom(AcidPlots,acid_coord_flip)
importFrom(AcidPlots,acid_geom_label_repel)
importFrom(AcidPlots,matchLabels)
importFrom(AcidPlots,plotCounts)
importFrom(AcidPlots,plotHeatmap)
importFrom(AcidPlots,plotPCA)
importFrom(AcidPlots,plotUpset)
importFrom(AcidPlots,scale_color_synesthesia_d)
importFrom(BiocGenerics,combine)
importFrom(BiocGenerics,plotMA)
importFrom(BiocGenerics,plotPCA)
importFrom(BiocGenerics,updateObject)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,counts)
importFrom(DESeq2,design)
importFrom(DESeq2,fpkm)
importFrom(DESeq2,nbinomWaldTest)
importFrom(DESeq2,priorInfo)
importFrom(IRanges,DataFrameList)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,as.data.frame)
importFrom(S4Vectors,cbind)
importFrom(S4Vectors,complete.cases)
importFrom(S4Vectors,cor)
importFrom(S4Vectors,do.call)
importFrom(S4Vectors,head)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,na.omit)
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(basejump,"interestingGroups<-")
importFrom(basejump,"metadata2<-")
importFrom(basejump,Gene2Symbol)
importFrom(basejump,as_tibble)
importFrom(basejump,autopadZeros)
importFrom(basejump,camelCase)
importFrom(basejump,convertSampleIDsToNames)
importFrom(basejump,correlation)
importFrom(basejump,decode)
importFrom(basejump,droplevels)
importFrom(basejump,import)
importFrom(basejump,initDir)
importFrom(basejump,interestingGroups)
importFrom(basejump,intersectionMatrix)
importFrom(basejump,leftJoin)
importFrom(basejump,makeNames)
importFrom(basejump,mapGenesToRownames)
importFrom(basejump,markdownHeader)
importFrom(basejump,markdownList)
importFrom(basejump,matchesGene2Symbol)
importFrom(basejump,melt)
importFrom(basejump,metadata2)
importFrom(basejump,printString)
importFrom(basejump,realpath)
importFrom(basejump,removeNA)
importFrom(basejump,requireNamespaces)
importFrom(basejump,showSlotInfo)
importFrom(basejump,snakeCase)
importFrom(basejump,standardizeCall)
importFrom(cli,cli_alert)
importFrom(cli,cli_alert_info)
importFrom(cli,cli_alert_warning)
importFrom(cli,cli_dl)
importFrom(cowplot,draw_plot)
importFrom(cowplot,ggdraw)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotation_logticks)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_density)
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,areDisjointSets)
importFrom(goalie,areIntersectingSets)
importFrom(goalie,areSameLength)
importFrom(goalie,areSetEqual)
importFrom(goalie,assert)
importFrom(goalie,bapply)
importFrom(goalie,hasLength)
importFrom(goalie,hasNames)
importFrom(goalie,hasRownames)
importFrom(goalie,hasRows)
importFrom(goalie,hasValidDimnames)
importFrom(goalie,hasValidNames)
importFrom(goalie,isAFile)
importFrom(goalie,isAlpha)
importFrom(goalie,isAny)
importFrom(goalie,isCharacter)
importFrom(goalie,isFlag)
importFrom(goalie,isGGScale)
importFrom(goalie,isHeaderLevel)
importFrom(goalie,isInRange)
importFrom(goalie,isInt)
importFrom(goalie,isNonNegative)
importFrom(goalie,isNumber)
importFrom(goalie,isPercentage)
importFrom(goalie,isPositive)
importFrom(goalie,isScalar)
importFrom(goalie,isString)
importFrom(goalie,isSubset)
importFrom(goalie,validate)
importFrom(knitr,kable)
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,setValidity)
importFrom(methods,show)
importFrom(methods,slot)
importFrom(methods,validObject)
importFrom(rlang,"!!")
importFrom(rlang,sym)
importFrom(scales,log_breaks)
importFrom(scales,pretty_breaks)
importFrom(stats,model.matrix)
importFrom(stats,relevel)
importFrom(stringr,str_locate_all)
importFrom(stringr,str_match)
importFrom(stringr,str_trunc)
importFrom(utils,capture.output)
importFrom(utils,getS3method)
importFrom(utils,packageName)
importFrom(utils,packageVersion)
importMethodsFrom(basejump,coerce)
