# Generated by roxygen2: do not edit by hand

export(COTAN)
export(DEAOnClusters)
export(ECDPlot)
export(GDIPlot)
export(UMAPPlot)
export(asClusterization)
export(automaticCOTANObjectCreation)
export(calculateG)
export(calculateGDI)
export(calculateGDIGivenCorr)
export(calculateGenesCE)
export(calculateLikelihoodOfObserved)
export(calculatePDI)
export(calculatePValue)
export(calculatePartialCoex)
export(calculateS)
export(cellSizePlot)
export(cellsHeatmapPlot)
export(cellsUMAPPlot)
export(cellsUniformClustering)
export(checkClusterUniformity)
export(checkersToDF)
export(cleanPlots)
export(clusterGeneContingencyTables)
export(clustersDeltaExpression)
export(clustersMarkersHeatmapPlot)
export(clustersSummaryData)
export(clustersSummaryPlot)
export(clustersTreePlot)
export(conditionsFromNames)
export(contingencyTables)
export(convertFromSingleCellExperiment)
export(convertToSingleCellExperiment)
export(datasetTags)
export(dfToCheckers)
export(distancesBetweenClusters)
export(establishGenesClusters)
export(estimatorsAreReady)
export(expectedContingencyTables)
export(expectedContingencyTablesNN)
export(expectedPartialContingencyTables)
export(expectedPartialContingencyTablesNN)
export(factorToVector)
export(findClustersMarkers)
export(fromClustersList)
export(geneSetEnrichment)
export(genesCoexSpace)
export(genesHeatmapPlot)
export(genesSelector)
export(genesSizePlot)
export(getClusters)
export(getColorsVector)
export(getColumnFromDF)
export(getLogNormData)
export(getMu)
export(getNormalizedData)
export(getNuNormData)
export(getProbabilityOfZero)
export(groupByClusters)
export(groupByClustersList)
export(heatmapPlot)
export(logFoldChangeOnClusters)
export(logThis)
export(mat2vec_rfast)
export(mergeClusters)
export(mergeUniformCellsClusters)
export(mitochondrialPercentagePlot)
export(multiMergeClusters)
export(niceFactorLevels)
export(normalizeNameAndLabels)
export(observedContingencyTables)
export(observedContingencyTablesYY)
export(observedPartialContingencyTables)
export(observedPartialContingencyTablesYY)
export(pValueFromDEA)
export(plotTheme)
export(reorderClusterization)
export(scatterPlot)
export(screePlot)
export(setColumnInDF)
export(setLoggingFile)
export(setLoggingLevel)
export(toClustersList)
export(vec2mat_rfast)
exportClasses(scCOTAN)
exportMethods(addClusterization)
exportMethods(addClusterizationCoex)
exportMethods(addCondition)
exportMethods(addElementToMetaDataset)
exportMethods(calculateCoex)
exportMethods(calculateThresholdShiftToUniformity)
exportMethods(checkObjIsUniform)
exportMethods(clean)
exportMethods(dropCellsCoex)
exportMethods(dropClusterization)
exportMethods(dropCondition)
exportMethods(dropGenesCells)
exportMethods(dropGenesCoex)
exportMethods(estimateDispersionBisection)
exportMethods(estimateDispersionNuBisection)
exportMethods(estimateLambdaLinear)
exportMethods(estimateNuLinear)
exportMethods(estimateNuLinearByCluster)
exportMethods(findFullyExpressedGenes)
exportMethods(findFullyExpressingCells)
exportMethods(flagNotFullyExpressedGenes)
exportMethods(flagNotFullyExpressingCells)
exportMethods(getAllConditions)
exportMethods(getCells)
exportMethods(getCellsCoex)
exportMethods(getCellsSize)
exportMethods(getCheckerThreshold)
exportMethods(getClusterizationData)
exportMethods(getClusterizationName)
exportMethods(getClusterizations)
exportMethods(getClustersCoex)
exportMethods(getCondition)
exportMethods(getConditionName)
exportMethods(getDims)
exportMethods(getDispersion)
exportMethods(getFullyExpressedGenes)
exportMethods(getFullyExpressingCells)
exportMethods(getGDI)
exportMethods(getGenes)
exportMethods(getGenesCoex)
exportMethods(getGenesSize)
exportMethods(getLambda)
exportMethods(getMetadataCells)
exportMethods(getMetadataDataset)
exportMethods(getMetadataElement)
exportMethods(getMetadataGenes)
exportMethods(getNu)
exportMethods(getNumCells)
exportMethods(getNumExpressedGenes)
exportMethods(getNumGenes)
exportMethods(getNumOfExpressingCells)
exportMethods(getRawData)
exportMethods(getZeroOneProj)
exportMethods(initializeMetaDataset)
exportMethods(isCoexAvailable)
exportMethods(proceedToCoex)
exportMethods(shiftCheckerThresholds)
exportMethods(storeGDI)
importClassesFrom(Matrix,dgCMatrix)
importClassesFrom(Matrix,dgeMatrix)
importClassesFrom(Matrix,dspMatrix)
importClassesFrom(Matrix,dsyMatrix)
importClassesFrom(Matrix,symmetricMatrix)
importFrom(BiocSingular,IrlbaParam)
importFrom(BiocSingular,runPCA)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,Legend)
importFrom(ComplexHeatmap,anno_barplot)
importFrom(ComplexHeatmap,anno_numeric)
importFrom(ComplexHeatmap,anno_text)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,crossprod)
importFrom(Matrix,forceSymmetric)
importFrom(Matrix,mean)
importFrom(Matrix,pack)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,t)
importFrom(Matrix,tcrossprod)
importFrom(RColorBrewer,brewer.pal)
importFrom(RColorBrewer,brewer.pal.info)
importFrom(Rfast,Crossprod)
importFrom(Rfast,Tcrossprod)
importFrom(Rfast,colSort)
importFrom(Rfast,colmeans)
importFrom(Rfast,colsums)
importFrom(Rfast,lower_tri)
importFrom(Rfast,lower_tri.assign)
importFrom(Rfast,rowsums)
importFrom(Rfast,transpose)
importFrom(Rfast,upper_tri)
importFrom(Rfast,upper_tri.assign)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(Seurat,Cells)
importFrom(Seurat,CreateSeuratObject)
importFrom(Seurat,Embeddings)
importFrom(Seurat,FindClusters)
importFrom(Seurat,FindNeighbors)
importFrom(Seurat,FindVariableFeatures)
importFrom(Seurat,Idents)
importFrom(Seurat,NormalizeData)
importFrom(Seurat,RunPCA)
importFrom(Seurat,RunUMAP)
importFrom(Seurat,ScaleData)
importFrom(Seurat,VariableFeatures)
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,colData)
importFrom(SingleCellExperiment,counts)
importFrom(SingleCellExperiment,rowData)
importFrom(SummarizedExperiment,assayNames)
importFrom(assertthat,assert_that)
importFrom(circlize,colorRamp2)
importFrom(dendextend,branches_color)
importFrom(dendextend,color_branches)
importFrom(dendextend,color_labels)
importFrom(dendextend,get_nodes_attr)
importFrom(dendextend,set)
importFrom(dplyr,filter)
importFrom(gghalves,geom_half_violin)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expansion)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_label)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,position_jitter)
importFrom(ggplot2,position_nudge)
importFrom(ggplot2,scale_color_gradient2)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_brewer)
importFrom(ggplot2,scale_fill_gradient2)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,unit)
importFrom(ggplot2,vars)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(ggrepel,geom_label_repel)
importFrom(ggrepel,geom_text_repel)
importFrom(ggthemes,theme_tufte)
importFrom(grDevices,colors)
importFrom(grDevices,dev.cur)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,par)
importFrom(graphics,title)
importFrom(grid,gpar)
importFrom(grid,grid.text)
importFrom(grid,unit)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setAs)
importFrom(methods,setIs)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(methods,validObject)
importFrom(parallel,mclapply)
importFrom(parallel,splitIndices)
importFrom(parallelDist,parDist)
importFrom(parallelly,availableCores)
importFrom(parallelly,supportsMulticore)
importFrom(proxy,dist)
importFrom(rlang,.data)
importFrom(rlang,is_character)
importFrom(rlang,is_double)
importFrom(rlang,is_empty)
importFrom(rlang,is_integer)
importFrom(rlang,is_list)
importFrom(rlang,is_logical)
importFrom(rlang,is_named2)
importFrom(rlang,is_null)
importFrom(rlang,is_string)
importFrom(rlang,is_vector)
importFrom(rlang,set_names)
importFrom(scales,math_format)
importFrom(scales,squish)
importFrom(scales,trans_breaks)
importFrom(scales,trans_format)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,cophenetic)
importFrom(stats,cutree)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,nlminb)
importFrom(stats,order.dendrogram)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,quantile)
importFrom(stats,symnum)
importFrom(stats,time)
importFrom(stringr,fixed)
importFrom(stringr,str_detect)
importFrom(stringr,str_equal)
importFrom(stringr,str_pad)
importFrom(stringr,str_remove)
importFrom(stringr,str_split_i)
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,"%>%")
importFrom(tidyr,all_of)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(utils,as.roman)
importFrom(utils,head)
importFrom(utils,tail)
importFrom(utils,write.csv)
importFrom(withr,local_options)
importFrom(withr,with_options)
importFrom(zeallot,"%->%")
importFrom(zeallot,"%<-%")