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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(cal.signatureScore.gdT.Fred)
export(calEffectSizeFromDE)
export(calProliferationScore)
export(convertLimmaToSCE)
export(fill.contamination)
export(inSilico.TCell)
export(inSilico.TGammaDelta)
export(make.geneTableLong)
export(render_KnitReport)
export(run.HVG)
export(run.Leiden)
export(run.Scanorama)
export(run.Seurat3)
export(run.inte.metaClust)
export(run.scanpy)
importFrom(Matrix,colMeans)
importFrom(Matrix,rowMeans)
importFrom(R.utils,loadToEnv)
importFrom(RColorBrewer,brewer.pal)
importFrom(RhpcBLASctl,omp_set_num_threads)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,`metadata<-`)
importFrom(S4Vectors,metadata)
importFrom(Seurat,AddModuleScore)
importFrom(Seurat,CellCycleScoring)
importFrom(Seurat,CreateSeuratObject)
importFrom(Seurat,DimPlot)
importFrom(Seurat,Embeddings)
importFrom(Seurat,FindClusters)
importFrom(Seurat,FindNeighbors)
importFrom(Seurat,FindVariableFeatures)
importFrom(Seurat,GetAssayData)
importFrom(Seurat,NoLegend)
importFrom(Seurat,ProjectDim)
importFrom(Seurat,RunPCA)
importFrom(Seurat,RunTSNE)
importFrom(Seurat,RunUMAP)
importFrom(Seurat,SCTransform)
importFrom(Seurat,ScaleData)
importFrom(Seurat,SetAssayData)
importFrom(Seurat,`VariableFeatures<-`)
importFrom(SingleCellExperiment,`reducedDim<-`)
importFrom(SingleCellExperiment,colData)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,rowData)
importFrom(SummarizedExperiment,`assay<-`)
importFrom(SummarizedExperiment,`colData<-`)
importFrom(SummarizedExperiment,`rowData<-`)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(cowplot,plot_grid)
importFrom(cowplot,save_plot)
importFrom(data.table,`:=`)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,dcast)
importFrom(data.table,fread)
importFrom(data.table,melt)
importFrom(data.table,setDT)
importFrom(doParallel,registerDoParallel)
importFrom(dplyr,arrange)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggpubr,ggboxplot)
importFrom(ggpubr,ggdensity)
importFrom(ggpubr,theme_pubr)
importFrom(grid,gpar)
importFrom(grid,unit)
importFrom(harmony,RunHarmony)
importFrom(leiden,leiden)
importFrom(magrittr,`%>%`)
importFrom(matrixStats,rowMedians)
importFrom(plyr,l_ply)
importFrom(plyr,ldply)
importFrom(plyr,llply)
importFrom(reticulate,import)
importFrom(rmarkdown,render)
importFrom(scran,buildSNNGraph)
importFrom(sscClust,classify.outlier)
importFrom(sscClust,effectsize)
importFrom(sscClust,integrate.by.avg)
importFrom(sscClust,rank.de.gene)
importFrom(sscClust,ssc.DEGene.limma)
importFrom(sscVis,collapseEffectSizeLong)
importFrom(sscVis,loginfo)
importFrom(sscVis,plotMatrix.simple)
importFrom(sscVis,ssc.average.cell)
importFrom(sscVis,ssc.build)
importFrom(sscVis,ssc.plot.heatmap)
importFrom(sscVis,ssc.plot.tsne)
importFrom(sscVis,ssc.plot.violin)
importFrom(sscVis,ssc.scale)
importFrom(sscVis,ssc.toLongTable)
importFrom(stats,median)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,pt)
importFrom(stats,qnorm)
importFrom(tibble,rownames_to_column)
importFrom(tictoc,tic)
importFrom(tictoc,toc)
importFrom(utils,data)
importFrom(utils,head)
importFrom(utils,str)
importFrom(utils,write.table)