# Generated by roxygen2: do not edit by hand

export("alphaThreshold<-")
export("collectionNames<-")
export("contrastNames<-")
export("nesThreshold<-")
export(AcidGSEATestsURL)
export(FGSEAList)
export(Gene2Symbol)
export(RankedList)
export(alphaThreshold)
export(collectionNames)
export(combine)
export(contrastNames)
export(convertToHuman)
export(enrichedGeneSets)
export(export)
export(geneSet)
export(geneSetNames)
export(geneSetResults)
export(leadingEdge)
export(markdownTables)
export(nesThreshold)
export(plotEnrichedGeneSets)
export(plotEnrichedUpset)
export(plotGeneSet)
export(plotHeatmap)
export(plotLFC)
export(plotNES)
export(prepareGeneSetFiles)
export(results)
export(updateObject)
exportClasses(FGSEAList)
exportClasses(RankedList)
exportMethods("alphaThreshold<-")
exportMethods("collectionNames<-")
exportMethods("contrastNames<-")
exportMethods("nesThreshold<-")
exportMethods(FGSEAList)
exportMethods(Gene2Symbol)
exportMethods(RankedList)
exportMethods(alphaThreshold)
exportMethods(collectionNames)
exportMethods(combine)
exportMethods(contrastNames)
exportMethods(convertToHuman)
exportMethods(enrichedGeneSets)
exportMethods(export)
exportMethods(geneSet)
exportMethods(geneSetNames)
exportMethods(geneSetResults)
exportMethods(leadingEdge)
exportMethods(markdownTables)
exportMethods(nesThreshold)
exportMethods(plotEnrichedGeneSets)
exportMethods(plotEnrichedUpset)
exportMethods(plotGeneSet)
exportMethods(plotHeatmap)
exportMethods(plotLFC)
exportMethods(plotNES)
exportMethods(results)
exportMethods(show)
exportMethods(updateObject)
importClassesFrom(DESeqAnalysis,DESeqAnalysis)
importFrom(AcidBase,basenameSansExt)
importFrom(AcidBase,initDir)
importFrom(AcidBase,methodFunction)
importFrom(AcidBase,realpath)
importFrom(AcidBase,showSlotInfo)
importFrom(AcidBase,standardizeCall)
importFrom(AcidCLI,abort)
importFrom(AcidCLI,alert)
importFrom(AcidCLI,alertInfo)
importFrom(AcidCLI,alertWarning)
importFrom(AcidCLI,dl)
importFrom(AcidCLI,toInlineString)
importFrom(AcidCLI,txt)
importFrom(AcidCLI,ul)
importFrom(AcidGenerics,"alphaThreshold<-")
importFrom(AcidGenerics,"collectionNames<-")
importFrom(AcidGenerics,"contrastNames<-")
importFrom(AcidGenerics,"nesThreshold<-")
importFrom(AcidGenerics,Gene2Symbol)
importFrom(AcidGenerics,alphaThreshold)
importFrom(AcidGenerics,as.DESeqDataSet)
importFrom(AcidGenerics,as.DataFrame)
importFrom(AcidGenerics,camelCase)
importFrom(AcidGenerics,collectionNames)
importFrom(AcidGenerics,contrastName)
importFrom(AcidGenerics,contrastNames)
importFrom(AcidGenerics,contrastSamples)
importFrom(AcidGenerics,convertToHuman)
importFrom(AcidGenerics,enrichedGeneSets)
importFrom(AcidGenerics,geneSet)
importFrom(AcidGenerics,geneSetNames)
importFrom(AcidGenerics,geneSetResults)
importFrom(AcidGenerics,leadingEdge)
importFrom(AcidGenerics,leftJoin)
importFrom(AcidGenerics,makeNames)
importFrom(AcidGenerics,mapGenesToRownames)
importFrom(AcidGenerics,markdownTables)
importFrom(AcidGenerics,melt)
importFrom(AcidGenerics,nesThreshold)
importFrom(AcidGenerics,plotEnrichedGeneSets)
importFrom(AcidGenerics,plotEnrichedUpset)
importFrom(AcidGenerics,plotGeneSet)
importFrom(AcidGenerics,plotHeatmap)
importFrom(AcidGenerics,plotLFC)
importFrom(AcidGenerics,plotNES)
importFrom(AcidGenerics,plotUpset)
importFrom(AcidGenerics,results)
importFrom(AcidGenerics,selectIf)
importFrom(AcidGenerics,showHeader)
importFrom(AcidGenerics,snakeCase)
importFrom(AcidGenerics,stripGeneVersions)
importFrom(AcidGenomes,mapHumanOrthologs)
importFrom(AcidMarkdown,markdownHeader)
importFrom(AcidPlots,.data)
importFrom(AcidPlots,acid_scale_color_discrete)
importFrom(AcidPlots,acid_scale_fill_discrete)
importFrom(AcidPlots,acid_theme_light)
importFrom(AcidPlots,matchLabels)
importFrom(BiocGenerics,"%in%")
importFrom(BiocGenerics,combine)
importFrom(BiocGenerics,lapply)
importFrom(BiocGenerics,order)
importFrom(BiocGenerics,organism)
importFrom(BiocGenerics,sort)
importFrom(BiocGenerics,unique)
importFrom(BiocGenerics,unlist)
importFrom(BiocGenerics,unsplit)
importFrom(BiocGenerics,updateObject)
importFrom(DESeqAnalysis,DESeqAnalysis)
importFrom(GenomeInfoDb,genome)
importFrom(GenomeInfoDb,seqnames)
importFrom(IRanges,IntegerList)
importFrom(IRanges,SplitDataFrameList)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,complete.cases)
importFrom(S4Vectors,decode)
importFrom(S4Vectors,head)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,na.omit)
importFrom(S4Vectors,split)
importFrom(S4Vectors,tail)
importFrom(SummarizedExperiment,"rowRanges<-")
importFrom(SummarizedExperiment,rowRanges)
importFrom(fgsea,calcGseaStat)
importFrom(fgsea,fgsea)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_alpha_identity)
importFrom(ggplot2,scale_shape_manual)
importFrom(goalie,allAreAtomic)
importFrom(goalie,allAreFiles)
importFrom(goalie,allAreMatchingRegex)
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,hasNoDuplicates)
importFrom(goalie,hasRownames)
importFrom(goalie,hasRows)
importFrom(goalie,isADir)
importFrom(goalie,isAFile)
importFrom(goalie,isAll)
importFrom(goalie,isAlpha)
importFrom(goalie,isAny)
importFrom(goalie,isBiocParallelParam)
importFrom(goalie,isCharacter)
importFrom(goalie,isFile)
importFrom(goalie,isFlag)
importFrom(goalie,isHeaderLevel)
importFrom(goalie,isInRange)
importFrom(goalie,isInstalled)
importFrom(goalie,isInt)
importFrom(goalie,isMatchingRegex)
importFrom(goalie,isNonNegative)
importFrom(goalie,isNumber)
importFrom(goalie,isOrganism)
importFrom(goalie,isScalar)
importFrom(goalie,isScalarInteger)
importFrom(goalie,isString)
importFrom(goalie,isSubset)
importFrom(goalie,requireNamespaces)
importFrom(goalie,validate)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,coerce)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setAs)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(methods,setValidity)
importFrom(methods,show)
importFrom(methods,slot)
importFrom(methods,validObject)
importFrom(pipette,export)
importFrom(pipette,import)
importFrom(stats,reorder)
importFrom(utils,packageName)
importFrom(utils,packageVersion)
importFrom(utils,sessionInfo)
importMethodsFrom(AcidBase,showHeader)
importMethodsFrom(AcidExperiment,Gene2Symbol)
importMethodsFrom(AcidExperiment,export)
importMethodsFrom(AcidExperiment,mapGenesToRownames)
importMethodsFrom(AcidGenomes,stripGeneVersions)
importMethodsFrom(AcidPlots,plotHeatmap)
importMethodsFrom(AcidPlots,plotUpset)
importMethodsFrom(AcidPlyr,leftJoin)
importMethodsFrom(AcidPlyr,melt)
importMethodsFrom(AcidPlyr,selectIf)
importMethodsFrom(DESeqAnalysis,as.DESeqDataSet)
importMethodsFrom(DESeqAnalysis,coerce)
importMethodsFrom(DESeqAnalysis,contrastName)
importMethodsFrom(DESeqAnalysis,contrastSamples)
importMethodsFrom(DESeqAnalysis,plotCounts)
importMethodsFrom(DESeqAnalysis,results)
importMethodsFrom(pipette,as.DataFrame)
importMethodsFrom(pipette,export)
importMethodsFrom(pipette,import)
importMethodsFrom(syntactic,camelCase)
importMethodsFrom(syntactic,makeNames)
importMethodsFrom(syntactic,snakeCase)
