scCancer/NAMESPACE at master · czythu/scCancer · GitHub

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# Generated by roxygen2: do not edit by hand

export(ConfusionMatrix)
export(CrossTest)
export(Entropy_test)
export(HRG)
export(Intergration)
export(Jaccard)
export(Kappa)
export(MarkerScore)
export(Read10Xdata)
export(SelectCells)
export(SelectGenes)
export(SimilarityHeatmap)
export(Spearman)
export(Test)
export(Train)
export(checkAnnoArguments)
export(checkCombArguments)
export(checkStatArguments)
export(clusterBarPlot)
export(confusion)
export(extractFiles)
export(genAnnoReport)
export(genStatReport)
export(generate10Xdata)
export(getCellTypeColor)
export(getDefaultColors)
export(getDefaultGeneSets)
export(getDefaultMarkers)
export(getTumorCluster)
export(ggplot_config)
export(markerPlot)
export(plotCellInteraction)
export(plotExprProgram)
export(plotGeneSet)
export(plotMalignancy)
export(plotSeurat)
export(pointDRPlot)
export(predCellType)
export(predMalignantCell)
export(predSubType)
export(prepareData)
export(prepareSeurat)
export(pro.core)
export(runCellClassify)
export(runCellCycle)
export(runCellInteraction)
export(runCellSubtypeClassify)
export(runDoublet)
export(runExprProgram)
export(runGeneSets)
export(runMalignancy)
export(runScAnnotation)
export(runScCombination)
export(runScStatistics)
export(runSeurat)
export(runStemness)
export(runSurvival)
export(select_fine_samples)
export(similarityCalculation)
export(trainAnnoModel)
export(trainSubAnnoModel)
exportClasses(cell_rules)
import(Biobase)
import(Matrix)
import(R.utils)
import(Seurat)
import(SoupX)
import(garnett)
import(ggplot2)
import(harmony)
import(knitr)
import(monocle)
import(org.Hs.eg.db)
import(rliger)
import(survival)
import(survminer)
import(xgboost)
importFrom(DESeq2,estimateSizeFactors)
importFrom(GSVA,gsva)
importFrom(NNLM,nnmf)
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(cowplot,get_legend)
importFrom(cowplot,plot_grid)
importFrom(dplyr,"%>%")
importFrom(dplyr,group_by)
importFrom(dplyr,top_n)
importFrom(garnett,check_markers)
importFrom(ggExtra,ggMarginal)
importFrom(ggpubr,ggarrange)
importFrom(grDevices,boxplot.stats)
importFrom(grDevices,colorRampPalette)
importFrom(grid,grid.draw)
importFrom(grid,grid.newpage)
importFrom(grid,unit.c)
importFrom(gridExtra,arrangeGrob)
importFrom(gridExtra,grid.arrange)
importFrom(markdown,markdownToHTML)
importFrom(methods,as)
importFrom(pheatmap,pheatmap)
importFrom(reshape2,melt)
importFrom(scds,bcds)
importFrom(scds,cxds)
importFrom(stats,cor)
importFrom(stats,density)
importFrom(stats,filter)
importFrom(stats,median)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stringr,str_c)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,write.csv)
importFrom(utils,write.table)