# Generated by roxygen2: do not edit by hand

export("bootstraps<-")
export("cellDist<-")
export("cellNames<-")
export("cellPairwiseDistances<-")
export("cpm<-")
export("featDist<-")
export("featureControlInfo<-")
export("featurePairwiseDistances<-")
export("fpkm<-")
export("is_exprs<-")
export("norm_counts<-")
export("norm_cpm<-")
export("norm_exprs<-")
export("norm_fpkm<-")
export("norm_tpm<-")
export("redDim<-")
export("reducedDimension<-")
export("setSpike<-")
export("set_exprs<-")
export("stand_exprs<-")
export("tpm<-")
export(areSizeFactorsCentred)
export(arrange)
export(arrange.SCESet)
export(bootstraps)
export(bootstraps.SCESet)
export(calcAverage)
export(calcIsExprs)
export(calculateCPM)
export(calculateFPKM)
export(calculateQCMetrics)
export(calculateTPM)
export(cellDist)
export(cellDistSCESet)
export(cellNames)
export(cellPairwiseDistances)
export(cellPairwiseDistances.SCESet)
export(counts.SCESet)
export(cpm)
export(cpmSCESet)
export(featDist)
export(featDistSCESet)
export(featureControlInfo)
export(featureControlInfo.SCESet)
export(featurePairwiseDistances)
export(featurePairwiseDistancesSCESet)
export(filter)
export(filter.SCESet)
export(findImportantPCs)
export(fpkm)
export(fpkm.SCESet)
export(fromCellDataSet)
export(getBMFeatureAnnos)
export(get_exprs)
export(get_exprs.SCESet)
export(isOutlier)
export(isSpike)
export(is_exprs)
export(is_exprs.SCESet)
export(mergeSCESet)
export(multiplot)
export(mutate)
export(mutate.SCESet)
export(newSCESet)
export(nexprs)
export(norm_counts)
export(norm_counts.SCESet)
export(norm_cpm)
export(norm_cpm.SCESet)
export(norm_exprs)
export(norm_exprs.SCESet)
export(norm_fpkm)
export(norm_fpkm.SCESet)
export(norm_tpm)
export(norm_tpm.SCESet)
export(normalise)
export(normaliseExprs)
export(normalize.SCESet)
export(normalizeExprs)
export(plotDiffusionMap)
export(plotDiffusionMapSCESet)
export(plotExplanatoryVariables)
export(plotExpression)
export(plotExpressionDefault)
export(plotExpressionSCESet)
export(plotExprsFreqVsMean)
export(plotExprsVsTxLength)
export(plotFeatureData)
export(plotHighestExprs)
export(plotMDS)
export(plotMDSSCESet)
export(plotMetadata)
export(plotPCASCESet)
export(plotPhenoData)
export(plotPlatePosition)
export(plotQC)
export(plotRLE)
export(plotReducedDim)
export(plotReducedDim.SCESet)
export(plotReducedDim.default)
export(plotSCESet)
export(plotTSNE)
export(read10XResults)
export(readKallistoResults)
export(readKallistoResultsOneSample)
export(readSalmonResults)
export(readSalmonResultsOneSample)
export(readTxResults)
export(redDim)
export(redDim.SCESet)
export(reducedDimension)
export(reducedDimension.SCESet)
export(rename)
export(rename.SCESet)
export(runKallisto)
export(runSalmon)
export(scater_gui)
export(sizeFactors.SCESet)
export(spikes)
export(stand_exprs)
export(stand_exprs.SCESet)
export(summariseExprsAcrossFeatures)
export(toCellDataSet)
export(tpm)
export(tpm.SCESet)
export(updateSCESet)
export(whichSpike)
export(writeSCESet)
exportClasses(SCESet)
exportMethods("[")
exportMethods("cellDist<-")
exportMethods("cellNames<-")
exportMethods("cellPairwiseDistances<-")
exportMethods("counts<-")
exportMethods("cpm<-")
exportMethods("fData<-")
exportMethods("fpkm<-")
exportMethods("is_exprs<-")
exportMethods("norm_counts<-")
exportMethods("norm_cpm<-")
exportMethods("norm_exprs<-")
exportMethods("norm_fpkm<-")
exportMethods("norm_tpm<-")
exportMethods("pData<-")
exportMethods("redDim<-")
exportMethods("reducedDimension<-")
exportMethods("setSpike<-")
exportMethods("set_exprs<-")
exportMethods("sizeFactors<-")
exportMethods("stand_exprs<-")
exportMethods("tpm<-")
exportMethods(arrange)
exportMethods(bootstraps)
exportMethods(cellDist)
exportMethods(cellPairwiseDistances)
exportMethods(counts)
exportMethods(cpm)
exportMethods(featDist)
exportMethods(featureControlInfo)
exportMethods(featurePairwiseDistances)
exportMethods(filter)
exportMethods(fpkm)
exportMethods(get_exprs)
exportMethods(isSpike)
exportMethods(is_exprs)
exportMethods(mutate)
exportMethods(norm_counts)
exportMethods(norm_cpm)
exportMethods(norm_exprs)
exportMethods(norm_fpkm)
exportMethods(norm_tpm)
exportMethods(normalize)
exportMethods(plot)
exportMethods(plotDiffusionMap)
exportMethods(plotExpression)
exportMethods(plotMDS)
exportMethods(plotPCA)
exportMethods(plotRLE)
exportMethods(plotReducedDim)
exportMethods(plotTSNE)
exportMethods(redDim)
exportMethods(reducedDimension)
exportMethods(rename)
exportMethods(sizeFactors)
exportMethods(spikes)
exportMethods(stand_exprs)
exportMethods(tpm)
exportMethods(whichSpike)
import(ggplot2)
import(methods)
import(shiny)
import(shinydashboard)
import(viridis)
importFrom(Biobase,"fData<-")
importFrom(Biobase,"pData<-")
importFrom(Biobase,"sampleNames<-")
importFrom(Biobase,"varMetadata<-")
importFrom(Biobase,'exprs<-')
importFrom(Biobase,AnnotatedDataFrame)
importFrom(Biobase,annotatedDataFrameFrom)
importFrom(Biobase,assayDataElement)
importFrom(Biobase,assayDataNew)
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(biomaRt,useMart)
importFrom(data.table,fread)
importFrom(dplyr,mutate)
importFrom(edgeR,calcNormFactors.default)
importFrom(edgeR,cpm.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(matrixStats,colCumsums)
importFrom(matrixStats,colVars)
importFrom(matrixStats,rowVars)
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,as.dist)
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)
useDynLib(scater, .registration=TRUE, .fixes="cxx_")
