NAMESPACE

# Generated by roxygen2: do not edit by hand

export(binarizeExp)
export(classify.outlier)
export(classifyCell.by.model)
export(classifyCell.by.sigGene)
export(collapseEffectSizeLong)
export(comb.pvalue)
export(cor.BLAS)
export(directEScombi)
export(directEScombiFromLongTable)
export(effectsize)
export(fftRtsne)
export(integrate.by.avg)
export(loginfo)
export(plotPairsCor)
export(plotSigGene)
export(rank.de.gene)
export(run.DE.matrix)
export(run.SC3)
export(run.cutree)
export(run.cutreeDynamic)
export(run.limma.matrix)
export(simple.removeBatchEffect)
export(ssc.DEGene.limma)
export(ssc.assay.hclust)
export(ssc.assay.zscore)
export(ssc.average.cell)
export(ssc.build)
export(ssc.clust)
export(ssc.clustSubsamplingClassification)
export(ssc.clusterMarkerGene)
export(ssc.displayName2id)
export(ssc.downsample)
export(ssc.id2displayName)
export(ssc.moduleScore)
export(ssc.order)
export(ssc.plot.GeneDensity)
export(ssc.plot.cor)
export(ssc.plot.heatmap)
export(ssc.plot.pca)
export(ssc.plot.silhouette)
export(ssc.plot.tsne)
export(ssc.plot.violin)
export(ssc.reduceDim)
export(ssc.run)
export(ssc.scale)
export(ssc.toLongTable)
export(ssc.variableGene)
importFrom(ADPclust,adpclust)
importFrom(BiocGenerics,t)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,multicoreWorkers)
importFrom(BiocParallel,register)
importFrom(MASS,ginv)
importFrom(Matrix,rowSums)
importFrom(RColorBrewer,brewer.pal)
importFrom(ROCR,performance)
importFrom(ROCR,prediction)
importFrom(RhpcBLASctl,omp_set_num_threads)
importFrom(Rtsne,Rtsne)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,`metadata<-`)
importFrom(S4Vectors,metadata)
importFrom(SC3,sc3)
importFrom(SC3,sc3_plot_cluster_stability)
importFrom(SC3,sc3_plot_consensus)
importFrom(SC3,sc3_plot_markers)
importFrom(SC3,sc3_plot_silhouette)
importFrom(SingleCellExperiment,`reducedDim<-`)
importFrom(SingleCellExperiment,`reducedDims<-`)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SummarizedExperiment,`assay<-`)
importFrom(SummarizedExperiment,`colData<-`)
importFrom(SummarizedExperiment,`rowData<-`)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(class,knn)
importFrom(data.table,`:=`)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,dcast)
importFrom(data.table,melt)
importFrom(data.table,setDT)
importFrom(data.table,setkey)
importFrom(densityClust,densityClust)
importFrom(densityClust,findClusters)
importFrom(doParallel,registerDoParallel)
importFrom(dplyr,inner_join)
importFrom(e1071,svm)
importFrom(factoextra,eclust)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,theme_bw)
importFrom(ggpubr,ggscatter)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(graphics,abline)
importFrom(graphics,curve)
importFrom(graphics,layout)
importFrom(graphics,lines)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,rect)
importFrom(grid,gpar)
importFrom(grid,unit)
importFrom(igraph,cluster_edge_betweenness)
importFrom(igraph,cluster_fast_greedy)
importFrom(igraph,cluster_infomap)
importFrom(igraph,cluster_label_prop)
importFrom(igraph,cluster_leading_eigen)
importFrom(igraph,cluster_louvain)
importFrom(igraph,cluster_optimal)
importFrom(igraph,cluster_spinglass)
importFrom(igraph,cluster_walktrap)
importFrom(leiden,leiden)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(matrixStats,rowMedians)
importFrom(matrixStats,rowVars)
importFrom(mclust,densityMclust)
importFrom(parallel,mclapply)
importFrom(plyr,l_ply)
importFrom(plyr,ldply)
importFrom(plyr,llply)
importFrom(randomForest,randomForest)
importFrom(ranger,ranger)
importFrom(scran,buildSNNGraph)
importFrom(scran,decomposeVar)
importFrom(scran,trendVar)
importFrom(sscVis,collapseEffectSizeLong)
importFrom(sscVis,cor.BLAS)
importFrom(sscVis,directEScombi)
importFrom(sscVis,directEScombiFromLongTable)
importFrom(sscVis,effectsize)
importFrom(sscVis,loginfo)
importFrom(sscVis,run.cutree)
importFrom(sscVis,run.cutreeDynamic)
importFrom(sscVis,simple.removeBatchEffect)
importFrom(sscVis,ssc.assay.hclust)
importFrom(sscVis,ssc.assay.zscore)
importFrom(sscVis,ssc.average.cell)
importFrom(sscVis,ssc.build)
importFrom(sscVis,ssc.displayName2id)
importFrom(sscVis,ssc.downsample)
importFrom(sscVis,ssc.id2displayName)
importFrom(sscVis,ssc.moduleScore)
importFrom(sscVis,ssc.order)
importFrom(sscVis,ssc.plot.GeneDensity)
importFrom(sscVis,ssc.plot.cor)
importFrom(sscVis,ssc.plot.heatmap)
importFrom(sscVis,ssc.plot.pca)
importFrom(sscVis,ssc.plot.silhouette)
importFrom(sscVis,ssc.plot.tsne)
importFrom(sscVis,ssc.plot.violin)
importFrom(sscVis,ssc.scale)
importFrom(sscVis,ssc.toLongTable)
importFrom(stats,TukeyHSD)
importFrom(stats,aggregate)
importFrom(stats,aov)
importFrom(stats,as.formula)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,dnorm)
importFrom(stats,fisher.test)
importFrom(stats,kmeans)
importFrom(stats,lm)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,pnorm)
importFrom(stats,ppoints)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(stats,qnorm)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stats,wilcox.test)
importFrom(utils,file_test)
importFrom(utils,head)
importFrom(utils,write.table)
importFrom(uwot,umap)
importFrom(varSelRF,varSelRF)