NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(BASiCSEstimate,SCESet)
S3method(BASiCSEstimate,matrix)
S3method(lun2Estimate,SingleCellExperiment)
S3method(lun2Estimate,matrix)
S3method(lunEstimate,SingleCellExperiment)
S3method(lunEstimate,matrix)
S3method(mfaEstimate,SingleCellExperiment)
S3method(mfaEstimate,matrix)
S3method(phenoEstimate,SingleCellExperiment)
S3method(phenoEstimate,matrix)
S3method(scDDEstimate,SingleCellExperiment)
S3method(scDDEstimate,default)
S3method(scDDEstimate,matrix)
S3method(simpleEstimate,SingleCellExperiment)
S3method(simpleEstimate,matrix)
S3method(splatEstimate,SingleCellExperiment)
S3method(splatEstimate,matrix)
S3method(zinbEstimate,SingleCellExperiment)
S3method(zinbEstimate,matrix)
export(BASiCSEstimate)
export(BASiCSSimulate)
export(addGeneLengths)
export(compareSCEs)
export(diffSCEs)
export(getParam)
export(getParams)
export(listSims)
export(lun2Estimate)
export(lun2Simulate)
export(lunEstimate)
export(lunSimulate)
export(makeCompPanel)
export(makeDiffPanel)
export(makeOverallPanel)
export(mfaEstimate)
export(mfaSimulate)
export(newBASiCSParams)
export(newLun2Params)
export(newLunParams)
export(newMFAParams)
export(newPhenoParams)
export(newSCDDParams)
export(newSimpleParams)
export(newSplatParams)
export(newZINBParams)
export(phenoEstimate)
export(phenoSimulate)
export(scDDEstimate)
export(scDDSimulate)
export(setParam)
export(setParams)
export(simpleEstimate)
export(simpleSimulate)
export(splatEstimate)
export(splatSimulate)
export(splatSimulateGroups)
export(splatSimulatePaths)
export(splatSimulateSingle)
export(summariseDiff)
export(zinbEstimate)
export(zinbSimulate)
exportClasses(BASiCSParams)
exportClasses(Lun2Params)
exportClasses(LunParams)
exportClasses(MFAParams)
exportClasses(PhenoParams)
exportClasses(SCDDParams)
exportClasses(SimpleParams)
exportClasses(SplatParams)
exportClasses(ZINBParams)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(SingleCellExperiment,"cpm<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(checkmate,checkCharacter)
importFrom(checkmate,checkClass)
importFrom(checkmate,checkDataFrame)
importFrom(checkmate,checkFactor)
importFrom(checkmate,checkFlag)
importFrom(checkmate,checkInt)
importFrom(checkmate,checkIntegerish)
importFrom(checkmate,checkNumber)
importFrom(checkmate,checkNumeric)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(locfit,locfit)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,callNextMethod)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(methods,validObject)
importFrom(stats,dnbinom)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,nls)
importFrom(stats,rbinom)
importFrom(stats,rchisq)
importFrom(stats,rgamma)
importFrom(stats,rlnorm)
importFrom(stats,rnbinom)
importFrom(stats,rnorm)
importFrom(stats,rpois)
importFrom(stats,runif)
importFrom(utils,head)