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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(Setup)
export(estimateParam)
export(estimateSpike)
export(evaluateDE)
export(evaluateDist)
export(evaluateROC)
export(evaluateSim)
export(plotEvalDE)
export(plotEvalDist)
export(plotEvalROC)
export(plotEvalSim)
export(plotParam)
export(plotSpike)
export(plotTime)
export(printEvalDE)
export(simulateDE)
import(ZIM)
importFrom(BPSC,BPglm)
importFrom(BiocGenerics,"sizeFactors<-")
importFrom(BiocGenerics,counts)
importFrom(BiocGenerics,estimateDispersions)
importFrom(BiocGenerics,sizeFactors)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bpparam)
importFrom(BiocParallel,register)
importFrom(DECENT,fitNoDE)
importFrom(DECENT,lrTest)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,counts)
importFrom(DESeq2,estimateDispersions)
importFrom(DESeq2,estimateSizeFactors)
importFrom(DESeq2,nbinomWaldTest)
importFrom(DESeq2,results)
importFrom(DESeq2,sizeFactors)
importFrom(DrImpute,DrImpute)
importFrom(DrImpute,preprocessSC)
importFrom(EBSeq,EBTest)
importFrom(EBSeq,MedianNorm)
importFrom(Hmisc,binconf)
importFrom(IHW,adj_pvalues)
importFrom(IHW,ihw)
importFrom(Linnorm,Linnorm.Norm)
importFrom(MASS,fitdistr)
importFrom(MASS,glm.nb)
importFrom(MASS,rlm)
importFrom(MAST,FromMatrix)
importFrom(MAST,lrTest)
importFrom(MAST,summary)
importFrom(Matrix,Matrix)
importFrom(NBPSeq,nbp.test)
importFrom(NOISeq,noiseqbio)
importFrom(NOISeq,readData)
importFrom(ROTS,ROTS)
importFrom(Rmagic,library.size.normalize)
importFrom(Rmagic,magic)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,mcols)
importFrom(SAVER,combine.saver)
importFrom(SAVER,saver)
importFrom(SCnorm,SCnorm)
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,altExp)
importFrom(SingleCellExperiment,sizeFactors)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,rowData)
importFrom(VGAM,negbinomial.size)
importFrom(bayNorm,BetaFun)
importFrom(bayNorm,bayNorm)
importFrom(baySeq,getLikelihoods)
importFrom(baySeq,getPriors.NB)
importFrom(baySeq,topCounts)
importFrom(broom,glance)
importFrom(cobs,cobs)
importFrom(cowplot,add_sub)
importFrom(cowplot,ggdraw)
importFrom(cowplot,plot_grid)
importFrom(data.table,data.table)
importFrom(doParallel,registerDoParallel)
importFrom(doParallel,stopImplicitCluster)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,count)
importFrom(dplyr,distinct)
importFrom(dplyr,do)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,inner_join)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_if)
importFrom(dplyr,n)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,summarise)
importFrom(dplyr,summarise_all)
importFrom(dplyr,ungroup)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,cpm)
importFrom(edgeR,cpm.DGEList)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,estimateGLMRobustDisp)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmLRT)
importFrom(edgeR,glmQLFTest)
importFrom(edgeR,glmQLFit)
importFrom(edgeR,thinCounts)
importFrom(edgeR,topTags)
importFrom(edgeR,zscoreNBinom)
importFrom(fitdistrplus,fitdist)
importFrom(fitdistrplus,gofstat)
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(future,plan)
importFrom(gamlss.dist,ZINBI)
importFrom(gamlss.dist,ZIP)
importFrom(ggplot2,aes_)
importFrom(ggplot2,alpha)
importFrom(ggplot2,annotate)
importFrom(ggplot2,annotation_logticks)
importFrom(ggplot2,as_labeller)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expand_scale)
importFrom(ggplot2,expansion)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_dotplot)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_pointrange)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,position_jitterdodge)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,stat_density2d)
importFrom(ggplot2,stat_summary)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_light)
importFrom(ggplot2,theme_linedraw)
importFrom(ggplot2,theme_minimal)
importFrom(ggpubr,ggtexttable)
importFrom(ggpubr,ttheme)
importFrom(ggstance,geom_linerangeh)
importFrom(grDevices,blues9)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,hcl)
importFrom(grid,unit)
importFrom(iCOBRA,COBRAData)
importFrom(iCOBRA,calculate_performance)
importFrom(kernlab,specc)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(magrittr,"%>%")
importFrom(matrixStats,rowSds)
importFrom(methods,is)
importFrom(methods,new)
importFrom(minpack.lm,nlsLM)
importFrom(moments,moment)
importFrom(monocle,differentialGeneTest)
importFrom(monocle,newCellDataSet)
importFrom(msir,loess.sd)
importFrom(nonnest2,vuongtest)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,mclapply)
importFrom(parallel,mcmapply)
importFrom(parallel,stopCluster)
importFrom(penalized,penalized)
importFrom(penalized,predict)
importFrom(plotrix,std.error)
importFrom(plyr,aaply)
importFrom(pscl,vuong)
importFrom(pscl,zeroinfl)
importFrom(qvalue,qvalue)
importFrom(reshape2,melt)
importFrom(rlang,.data)
importFrom(rsvd,rpca)
importFrom(scDD,scDD)
importFrom(scales,math_format)
importFrom(scales,percent)
importFrom(scales,trans_breaks)
importFrom(scales,trans_format)
importFrom(scater,isOutlier)
importFrom(scone,SconeExperiment)
importFrom(scone,estimate_ziber)
importFrom(scone,impute_expectation)
importFrom(scone,scone)
importFrom(scran,calculateSumFactors)
importFrom(scran,computeSumFactors)
importFrom(scran,quickCluster)
importFrom(sctransform,correct)
importFrom(sctransform,vst)
importFrom(scuttle,computeSpikeFactors)
importFrom(stats,AIC)
importFrom(stats,aggregate)
importFrom(stats,approx)
importFrom(stats,approxfun)
importFrom(stats,coefficients)
importFrom(stats,complete.cases)
importFrom(stats,density)
importFrom(stats,dgamma)
importFrom(stats,dnbinom)
importFrom(stats,dnorm)
importFrom(stats,dpois)
importFrom(stats,ecdf)
importFrom(stats,family)
importFrom(stats,fitted)
importFrom(stats,glm)
importFrom(stats,lm)
importFrom(stats,logLik)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.exclude)
importFrom(stats,na.omit)
importFrom(stats,nls.control)
importFrom(stats,p.adjust)
importFrom(stats,p.adjust.methods)
importFrom(stats,pchisq)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,rbeta)
importFrom(stats,rbinom)
importFrom(stats,reorder)
importFrom(stats,residuals)
importFrom(stats,rgamma)
importFrom(stats,rnbinom)
importFrom(stats,rnorm)
importFrom(stats,rpois)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,t.test)
importFrom(stats,uniroot)
importFrom(stats,var)
importFrom(stats,weighted.mean)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,"%>%")
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,separate)
importFrom(truncnorm,rtruncnorm)
importFrom(utils,capture.output)
importFrom(utils,stack)
importFrom(utils,tail)
importFrom(zinbwave,computeObservationalWeights)
importFrom(zinbwave,glmWeightedF)
importFrom(zinbwave,zinbFit)
importFrom(zingeR,glmWeightedF)
importFrom(zingeR,zeroWeightsLS)
importMethodsFrom(DESeq2,sizeFactors)
importMethodsFrom(baySeq,libsizes)