# Generated by roxygen2: do not edit by hand

export(DESeqAnalysis)
export(DESeqAnalysisList)
export(alphaSummary)
export(contrastName)
export(contrastSamples)
export(deg)
export(export)
export(importPairwiseContrasts)
export(lfcShrinkType)
export(markdown)
export(plotBaseMean)
export(plotCounts)
export(plotDEGHeatmap)
export(plotDEGPCA)
export(plotDEGUpset)
export(plotMA)
export(plotMeanAverage)
export(plotPCA)
export(plotVolcano)
export(results)
export(resultsMatrix)
export(resultsNames)
export(resultsTables)
export(sampleData)
export(topTables)
export(transformType)
exportClasses(DESeqAnalysis)
exportClasses(DESeqAnalysisList)
exportMethods(alphaSummary)
exportMethods(coerce)
exportMethods(contrastName)
exportMethods(contrastSamples)
exportMethods(deg)
exportMethods(export)
exportMethods(lfcShrinkType)
exportMethods(markdown)
exportMethods(plotBaseMean)
exportMethods(plotCounts)
exportMethods(plotDEGHeatmap)
exportMethods(plotDEGPCA)
exportMethods(plotDEGUpset)
exportMethods(plotMA)
exportMethods(plotPCA)
exportMethods(plotVolcano)
exportMethods(results)
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(BiocGenerics,plotMA)
importFrom(BiocGenerics,plotPCA)
importFrom(BiocGenerics,updateObject)
importFrom(DESeq2,counts)
importFrom(DESeq2,priorInfo)
importFrom(IRanges,DataFrameList)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,as.data.frame)
importFrom(S4Vectors,cbind)
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(UpSetR,fromList)
importFrom(acidplots,acid_geom_label_repel)
importFrom(acidplots,plotCounts)
importFrom(acidplots,plotHeatmap)
importFrom(acidplots,plotPCA)
importFrom(acidplots,scale_colour_synesthesia_d)
importFrom(acidplots,upset)
importFrom(basejump,"interestingGroups<-")
importFrom(basejump,Gene2Symbol)
importFrom(basejump,as_tibble)
importFrom(basejump,camelCase)
importFrom(basejump,convertSampleIDsToNames)
importFrom(basejump,decode)
importFrom(basejump,droplevels)
importFrom(basejump,import)
importFrom(basejump,initDir)
importFrom(basejump,leftJoin)
importFrom(basejump,makeNames)
importFrom(basejump,mapGenesToRownames)
importFrom(basejump,markdownHeader)
importFrom(basejump,markdownList)
importFrom(basejump,matchArgsToDoCall)
importFrom(basejump,matchInterestingGroups)
importFrom(basejump,matchesGene2Symbol)
importFrom(basejump,methodFormals)
importFrom(basejump,printString)
importFrom(basejump,removeNA)
importFrom(basejump,showSlotInfo)
importFrom(basejump,snakeCase)
importFrom(basejump,standardizeCall)
importFrom(bioverbs,alphaSummary)
importFrom(bioverbs,contrastName)
importFrom(bioverbs,contrastSamples)
importFrom(bioverbs,deg)
importFrom(bioverbs,export)
importFrom(bioverbs,markdown)
importFrom(bioverbs,plotCounts)
importFrom(bioverbs,plotDEGHeatmap)
importFrom(bioverbs,plotDEGPCA)
importFrom(bioverbs,plotDEGUpset)
importFrom(bioverbs,plotVolcano)
importFrom(bioverbs,results)
importFrom(bioverbs,resultsMatrix)
importFrom(bioverbs,resultsNames)
importFrom(bioverbs,resultsTables)
importFrom(bioverbs,sampleData)
importFrom(bioverbs,topTables)
importFrom(cowplot,draw_plot)
importFrom(cowplot,ggdraw)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotation_logticks)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(goalie,areDisjointSets)
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,isHeaderLevel)
importFrom(goalie,isInRange)
importFrom(goalie,isInt)
importFrom(goalie,isNonEmpty)
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,show)
importFrom(methods,slot)
importFrom(methods,validObject)
importFrom(rlang,"!!")
importFrom(rlang,sym)
importFrom(scales,log_breaks)
importFrom(scales,pretty_breaks)
importFrom(stringr,str_match)
importFrom(stringr,str_trunc)
importFrom(utils,capture.output)
importFrom(utils,getS3method)
importFrom(utils,globalVariables)
importFrom(utils,packageVersion)
importMethodsFrom(basejump,coerce)
