# Generated by roxygen2: do not edit by hand

export("bootstraps<-")
export("fpkm<-")
export("norm_exprs<-")
export("stand_exprs<-")
export(areSizeFactorsCentred)
export(arrange)
export(bootstraps)
export(calcAverage)
export(calcIsExprs)
export(calculateCPM)
export(calculateFPKM)
export(calculateQCMetrics)
export(calculateTPM)
export(downsampleCounts)
export(exprs)
export(filter)
export(findImportantPCs)
export(fpkm)
export(fromCellDataSet)
export(getBMFeatureAnnos)
export(isOutlier)
export(multiplot)
export(mutate)
export(newSCESet)
export(nexprs)
export(norm_exprs)
export(normalise)
export(normaliseExprs)
export(normalizeExprs)
export(normalizeSCE)
export(plotCellData)
export(plotColData)
export(plotDiffusionMap)
export(plotExplanatoryVariables)
export(plotExpression)
export(plotExpressionDefault)
export(plotExprsFreqVsMean)
export(plotExprsVsTxLength)
export(plotFeatureData)
export(plotHighestExprs)
export(plotMDS)
export(plotMetadata)
export(plotPCASCE)
export(plotPhenoData)
export(plotPlatePosition)
export(plotQC)
export(plotRLE)
export(plotReducedDim)
export(plotReducedDimDefault)
export(plotRowData)
export(plotScater)
export(plotTSNE)
export(read10XResults)
export(read10xResults)
export(readKallistoResults)
export(readKallistoResultsOneSample)
export(readSalmonResults)
export(readSalmonResultsOneSample)
export(readTxResults)
export(rename)
export(runDiffusionMap)
export(runKallisto)
export(runPCA)
export(runSalmon)
export(runTSNE)
export(scater_gui)
export(stand_exprs)
export(summariseExprsAcrossFeatures)
export(toCellDataSet)
export(toSingleCellExperiment)
export(updateSCESet)
exportClasses(SCESet)
exportMethods(arrange)
exportMethods(bootstraps)
exportMethods(filter)
exportMethods(mutate)
exportMethods(normalize)
exportMethods(plotPCA)
exportMethods(rename)
import(Matrix)
import(SingleCellExperiment)
import(ggplot2)
import(shiny)
import(shinydashboard)
import(viridis)
importClassesFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(Biobase,"assayDataElement<-")
importFrom(Biobase,"sampleNames<-")
importFrom(Biobase,"varMetadata<-")
importFrom(Biobase,'exprs<-')
importFrom(Biobase,assayDataElement)
importFrom(Biobase,exprs)
importFrom(Biobase,fData)
importFrom(Biobase,featureData)
importFrom(Biobase,featureNames)
importFrom(Biobase,pData)
importFrom(Biobase,phenoData)
importFrom(Biobase,sampleNames)
importFrom(Biobase,varLabels)
importFrom(BiocGenerics,"counts<-")
importFrom(BiocGenerics,"sizeFactors<-")
importFrom(BiocGenerics,counts)
importFrom(BiocGenerics,normalize)
importFrom(BiocGenerics,plotPCA)
importFrom(BiocGenerics,sizeFactors)
importFrom(Matrix,readMM)
importFrom(Rcpp,sourceCpp)
importFrom(S4Vectors,'metadata<-')
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,metadata)
importFrom(SingleCellExperiment,"cpm<-")
importFrom(SingleCellExperiment,"logcounts<-")
importFrom(SingleCellExperiment,"normcounts<-")
importFrom(SingleCellExperiment,"tpm<-")
importFrom(SingleCellExperiment,cpm)
importFrom(SingleCellExperiment,logcounts)
importFrom(SingleCellExperiment,normcounts)
importFrom(SingleCellExperiment,tpm)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(biomaRt,useMart)
importFrom(data.table,fread)
importFrom(dplyr,mutate)
importFrom(edgeR,calcNormFactors.default)
importFrom(ggbeeswarm,geom_quasirandom)
importFrom(grid,grid.layout)
importFrom(grid,grid.newpage)
importFrom(grid,pushViewport)
importFrom(grid,viewport)
importFrom(limma,lmFit)
importFrom(limma,residuals.MArrayLM)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(parallel,makeCluster)
importFrom(parallel,parLapply)
importFrom(parallel,stopCluster)
importFrom(plyr,aaply)
importFrom(reshape2,melt)
importFrom(rhdf5,H5close)
importFrom(rhdf5,h5read)
importFrom(rjson,fromJSON)
importFrom(stats,cmdscale)
importFrom(stats,coef)
importFrom(stats,dist)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,nls)
importFrom(stats,prcomp)
importFrom(stats,quantile)
importFrom(stats,var)
importFrom(tximport,tximport)
importFrom(utils,read.delim)
importFrom(utils,read.table)
useDynLib(scater, .registration=TRUE, .fixes="cxx_")
