NAMESPACE

# Generated by roxygen2: do not edit by hand

export(bcbioSingleCell)
export(bcbioSingleCellTestsUrl)
export(calculateMetrics)
export(filterCells)
export(plotBarcodeRanks)
export(plotCellCounts)
export(plotCountsPerCell)
export(plotCountsVsFeatures)
export(plotFeaturesPerCell)
export(plotMitoRatio)
export(plotNovelty)
export(plotQc)
export(plotReadsPerCell)
export(show)
export(updateObject)
exportClasses(bcbioSingleCell)
exportMethods("[")
exportMethods(plotReadsPerCell)
exportMethods(show)
exportMethods(updateObject)
importClassesFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(AcidBase,metricsCols)
importFrom(AcidBase,printString)
importFrom(AcidBase,realpath)
importFrom(AcidBase,showSlotInfo)
importFrom(AcidBase,standardizeCall)
importFrom(AcidBase,strMatch)
importFrom(AcidCLI,abort)
importFrom(AcidCLI,alert)
importFrom(AcidCLI,alertSuccess)
importFrom(AcidCLI,alertWarning)
importFrom(AcidCLI,h1)
importFrom(AcidCLI,h2)
importFrom(AcidCLI,separator)
importFrom(AcidCLI,toInlineString)
importFrom(AcidExperiment,detectLanes)
importFrom(AcidExperiment,droplevels2)
importFrom(AcidExperiment,importSampleData)
importFrom(AcidExperiment,matchInterestingGroups)
importFrom(AcidExperiment,minimalSampleData)
importFrom(AcidExperiment,sampleNames)
importFrom(AcidGenerics,"interestingGroups<-")
importFrom(AcidGenerics,calculateMetrics)
importFrom(AcidGenerics,camelCase)
importFrom(AcidGenerics,droplevels2)
importFrom(AcidGenerics,filterCells)
importFrom(AcidGenerics,interestingGroups)
importFrom(AcidGenerics,leftJoin)
importFrom(AcidGenerics,makeDimnames)
importFrom(AcidGenerics,makeLabel)
importFrom(AcidGenerics,makeNames)
importFrom(AcidGenerics,metrics)
importFrom(AcidGenerics,plotBarcodeRanks)
importFrom(AcidGenerics,plotCellCounts)
importFrom(AcidGenerics,plotCountsPerCell)
importFrom(AcidGenerics,plotCountsVsFeatures)
importFrom(AcidGenerics,plotFeaturesPerCell)
importFrom(AcidGenerics,plotMitoRatio)
importFrom(AcidGenerics,plotNovelty)
importFrom(AcidGenerics,plotQc)
importFrom(AcidGenerics,plotReadsPerCell)
importFrom(AcidGenerics,sampleData)
importFrom(AcidGenomes,emptyRanges)
importFrom(AcidGenomes,makeGRangesFromEnsembl)
importFrom(AcidGenomes,makeGRangesFromGff)
importFrom(AcidMarkdown,markdownPlots)
importFrom(AcidPlots,"!!!")
importFrom(AcidPlots,.data)
importFrom(AcidPlots,acid_geom_abline)
importFrom(AcidPlots,acid_geom_label)
importFrom(AcidPlots,acid_geom_label_average)
importFrom(AcidPlots,acid_geom_label_repel)
importFrom(AcidPlots,acid_scale_color_discrete)
importFrom(AcidPlots,acid_scale_fill_discrete)
importFrom(AcidPlots,syms)
importFrom(AcidSingleCell,makeSingleCellExperiment)
importFrom(AcidSingleCell,mapCellsToSamples)
importFrom(BiocGenerics,counts)
importFrom(BiocGenerics,updateObject)
importFrom(IRanges,DataFrameList)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,cbind)
importFrom(S4Vectors,do.call)
importFrom(S4Vectors,droplevels)
importFrom(S4Vectors,lapply)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,"rowRanges<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(bcbioBase,getBarcodeCutoffFromCommands)
importFrom(bcbioBase,getGtfFileFromYaml)
importFrom(bcbioBase,getLevelFromCommands)
importFrom(bcbioBase,getSampleDataFromYaml)
importFrom(bcbioBase,getUmiTypeFromCommands)
importFrom(bcbioBase,importDataVersions)
importFrom(bcbioBase,importProgramVersions)
importFrom(bcbioBase,projectDir)
importFrom(bcbioBase,runDate)
importFrom(bcbioBase,sampleDirs)
importFrom(ggplot2,aes)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_step)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,stat_ecdf)
importFrom(ggplot2,vars)
importFrom(ggridges,geom_density_ridges)
importFrom(goalie,allAreDirectories)
importFrom(goalie,allAreFiles)
importFrom(goalie,areDisjointSets)
importFrom(goalie,areSetEqual)
importFrom(goalie,assert)
importFrom(goalie,hasLength)
importFrom(goalie,hasNames)
importFrom(goalie,hasRownames)
importFrom(goalie,hasValidDimnames)
importFrom(goalie,isADirectory)
importFrom(goalie,isAFile)
importFrom(goalie,isAUrl)
importFrom(goalie,isAny)
importFrom(goalie,isCharacter)
importFrom(goalie,isDirectory)
importFrom(goalie,isFile)
importFrom(goalie,isFlag)
importFrom(goalie,isInt)
importFrom(goalie,isString)
importFrom(goalie,isSubset)
importFrom(goalie,requireNamespaces)
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,setClass)
importFrom(methods,show)
importFrom(methods,slot)
importFrom(methods,validObject)
importFrom(parallel,mcMap)
importFrom(parallel,mclapply)
importFrom(pipette,import)
importFrom(utils,capture.output)
importFrom(utils,packageName)
importFrom(utils,packageVersion)
importMethodsFrom(AcidExperiment,"interestingGroups<-")
importMethodsFrom(AcidExperiment,calculateMetrics)
importMethodsFrom(AcidExperiment,interestingGroups)
importMethodsFrom(AcidExperiment,metrics)
importMethodsFrom(AcidExperiment,sampleData)
importMethodsFrom(AcidExperiment,sampleNames)
importMethodsFrom(AcidPlyr,leftJoin)
importMethodsFrom(AcidSingleCell,sampleData)
importMethodsFrom(pipette,import)
importMethodsFrom(syntactic,camelCase)
importMethodsFrom(syntactic,makeDimnames)
importMethodsFrom(syntactic,makeLabel)
importMethodsFrom(syntactic,makeNames)