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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export("%JCS%")
export("%MCD%")
export("cellIDs<-")
export("complexityCutoff<-")
export("expressionCutoff<-")
export("geneIDs<-")
export("housekeepingCutoff<-")
export("logBase<-")
export("logtpm<-")
export("mpMap<-")
export("nodeID<-")
export("pseudoCount<-")
export("qualityControl<-")
export("scalingFactor<-")
export("statsQC<-")
export("typeMatrix<-")
export(DefaultPreprocConfig)
export(NucseqPreprocConfig)
export(PreprocConfig)
export(QCResults)
export(SCANDAL_G1S_MARKERS)
export(SCANDAL_G2M_MARKERS)
export(SCANDAL_HOUSEKEEPING_GENES_LIST)
export(SCANDAL_IDH_A_AC_MARKERS)
export(SCANDAL_IDH_A_G1S_MARKERS)
export(SCANDAL_IDH_A_G2M_MARKERS)
export(SCANDAL_IDH_A_OC_MARKERS)
export(SCANDAL_IDH_A_STEMNESS_MARKERS)
export(SCANDAL_IDH_O_AC_MARKERS)
export(SCANDAL_IDH_O_G1S_MARKERS)
export(SCANDAL_IDH_O_G2M_MARKERS)
export(SCANDAL_IDH_O_OC_MARKERS)
export(SCANDAL_IDH_O_STEMNESS_MARKERS)
export(SCANDAL_MACROPHAGE_MARKERS)
export(SCANDAL_OLIGODENDROCYTE_MARKERS)
export(SS2PreprocConfig)
export(ScandalDataSet)
export(ScandalMetaprograms)
export(cell2SampleMap)
export(cellIDs)
export(center_matrix)
export(colTbl)
export(complexityCutoff)
export(compute_complexity)
export(compute_housekeeping)
export(compute_louvain_clusters)
export(consensusClusters)
export(corL2R)
export(count_genes_per_chromosome)
export(expressionCutoff)
export(geneIDs)
export(housekeepingCutoff)
export(inspectSamples)
export(l2R)
export(load_dataset)
export(load_gene_pos_file)
export(logBase)
export(log_transform)
export(logtpm)
export(metaPrograms)
export(mpAssigned)
export(mpL2R)
export(mpMap)
export(mpScores)
export(nmf_extract_programs)
export(nmf_run)
export(nodeID)
export(prepare_nmf_matrix)
export(prepare_samples)
export(preprocConfig)
export(preprocess_matrix)
export(projectID)
export(pseudoCount)
export(qualityControl)
export(reverse_log_transform)
export(sampleIDs)
export(scalingFactor)
export(scandal_cell_complexity_distribution_plot)
export(scandal_cell_qc_data)
export(scandal_cluster_markers_density)
export(scandal_cna_classify_cells)
export(scandal_cna_classify_scores)
export(scandal_cna_compute_matrix)
export(scandal_cna_compute_scores)
export(scandal_cna_get_malignant_cells)
export(scandal_cna_infer)
export(scandal_cna_plot)
export(scandal_cna_scores_plot)
export(scandal_complexity_distribution_plot)
export(scandal_default_umap_config)
export(scandal_gene_qc_data)
export(scandal_histogram_plot)
export(scandal_inspect_samples)
export(scandal_load_data)
export(scandal_markers_plot)
export(scandal_mean_expression_frequency_plot)
export(scandal_mean_housekeeping_expression_plot)
export(scandal_metaprograms)
export(scandal_plot)
export(scandal_plot_qc_metrics)
export(scandal_preprocess)
export(scandal_quality_control_stats)
export(scandal_reduced_dims_plot)
export(scandal_save_data)
export(scandal_scatter_plot)
export(scandal_setup_analysis)
export(scandal_simple_heatmap_plot)
export(scandal_tsne_plot)
export(scandal_umap_plot)
export(scandal_whiskers_plot)
export(scoreThreshold)
export(scoringStrategy)
export(statsQC)
export(typeMatrix)
export(umi2upm)
export(unprocessedData)
export(wsPrograms)
export(wsScores)
exportClasses(PreprocConfig)
exportClasses(QCResults)
exportClasses(ScandalDataSet)
exportClasses(ScandalMetaprograms)
exportMethods("cellIDs<-")
exportMethods("complexityCutoff<-")
exportMethods("expressionCutoff<-")
exportMethods("geneIDs<-")
exportMethods("housekeepingCutoff<-")
exportMethods("logBase<-")
exportMethods("logtpm<-")
exportMethods("mpMap<-")
exportMethods("nodeID<-")
exportMethods("pseudoCount<-")
exportMethods("qualityControl<-")
exportMethods("scalingFactor<-")
exportMethods("statsQC<-")
exportMethods("typeMatrix<-")
exportMethods(cell2SampleMap)
exportMethods(cellIDs)
exportMethods(colTbl)
exportMethods(complexityCutoff)
exportMethods(consensusClusters)
exportMethods(corL2R)
exportMethods(expressionCutoff)
exportMethods(geneIDs)
exportMethods(housekeepingCutoff)
exportMethods(inspectSamples)
exportMethods(l2R)
exportMethods(logBase)
exportMethods(logtpm)
exportMethods(metaPrograms)
exportMethods(mpAssigned)
exportMethods(mpL2R)
exportMethods(mpMap)
exportMethods(mpScores)
exportMethods(nodeID)
exportMethods(preprocConfig)
exportMethods(projectID)
exportMethods(pseudoCount)
exportMethods(qualityControl)
exportMethods(sampleIDs)
exportMethods(scalingFactor)
exportMethods(scoreThreshold)
exportMethods(scoringStrategy)
exportMethods(show)
exportMethods(statsQC)
exportMethods(typeMatrix)
exportMethods(unprocessedData)
exportMethods(wsPrograms)
exportMethods(wsScores)
import(Matrix)
import(SingleCellExperiment)
import(SummarizedExperiment)
import(ggplot2)
import(patchwork)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(S4Vectors,SimpleList)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,decorate_heatmap_body)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(ConsensusClusterPlus,ConsensusClusterPlus)
importFrom(ConsensusClusterPlus,calcICL)
importFrom(FNN,get.knn)
importFrom(NMF,basis)
importFrom(NMF,nmf)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(caTools,runmean)
importFrom(circlize,colorRamp2)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,desc)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,pull)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(grDevices,dev.off)
importFrom(grDevices,jpeg)
importFrom(grid,gpar)
importFrom(grid,grid.lines)
importFrom(igraph,cluster_louvain)
importFrom(igraph,graph_from_data_frame)
importFrom(igraph,membership)
importFrom(igraph,simplify)
importFrom(infercna,splitGenes)
importFrom(matrixStats,colSds)
importFrom(methods,as)
importFrom(methods,callNextMethod)
importFrom(methods,is)
importFrom(methods,new)
importFrom(reshape2,melt)
importFrom(scales,hue_pal)
importFrom(scales,squish)
importFrom(scalop,score)
importFrom(stats,cor)
importFrom(stats,median)
importFrom(stats,quantile)
importFrom(stats,setNames)
importFrom(tibble,as_tibble)
importFrom(tibble,is_tibble)
importFrom(tibble,tibble)
importFrom(utils,read.delim)