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[ "celdaPerplexity" ] }, { "page": "celdaPerplexity-celdaList-method", "title": "Get perplexity for every model in a celdaList", "topics": [ "celdaPerplexity,celdaList-method" ] }, { "page": "celdaProbabilityMap", "title": "Probability map for a celda model", "topics": [ "celdaProbabilityMap", "celdaProbabilityMap,SingleCellExperiment-method" ] }, { "page": "celdatosce", "title": "Convert old celda model object to 'SCE' object", "topics": [ "celdatosce", "celdatosce,celdaList-method", "celdatosce,celda_C-method", "celdatosce,celda_CG-method", "celdatosce,celda_G-method" ] }, { "page": "celdaTsne", "title": "t-Distributed Stochastic Neighbor Embedding (t-SNE) dimension reduction for celda 'sce' object", "topics": [ "celdaTsne", "celdaTsne,SingleCellExperiment-method" ] }, { "page": "celdaUmap", "title": "Uniform Manifold Approximation and Projection (UMAP) dimension reduction for celda 'sce' object", "topics": [ "celdaUmap", "celdaUmap,SingleCellExperiment-method" ] }, { "page": "clusterProbability", "title": "Get the conditional probabilities of cell in subpopulations from celda model", "topics": [ "clusterProbability", "clusterProbability,SingleCellExperiment-method" ] }, { "page": "compareCountMatrix", "title": "Check count matrix consistency", "topics": [ "compareCountMatrix", "compareCountMatrix,ANY,celdaList-method", "compareCountMatrix,ANY,celdaModel-method" ] }, { "page": "contaminationSim", "title": "contaminationSim", "topics": [ "contaminationSim" ] }, { "page": "countChecksum", "title": "Get the MD5 hash of the count matrix from the celdaList", "topics": [ "countChecksum" ] }, { "page": "countChecksum-celdaList-method", "title": "Get the MD5 hash of the count matrix from the celdaList", "topics": [ "countChecksum,celdaList-method" ] }, { "page": "decontX", "title": "Contamination estimation with decontX", "topics": [ "decontX", "decontX,ANY-method", "decontX,SingleCellExperiment-method" ] }, { "page": "decontXcounts", "title": "Get or set decontaminated counts matrix", "topics": [ "decontXcounts", "decontXcounts,SingleCellExperiment-method", "decontXcounts<-", "decontXcounts<-,SingleCellExperiment-method" ] }, { "page": "distinctColors", "title": "Create a color palette", "topics": [ "distinctColors" ] }, { "page": "eigenMatMultInt", "title": "Fast matrix multiplication for double x int", "topics": [ "eigenMatMultInt" ] }, { "page": "eigenMatMultNumeric", "title": "Fast matrix multiplication for double x double", "topics": [ "eigenMatMultNumeric" ] }, { "page": "factorizeMatrix", "title": "Generate factorized matrices showing each feature's influence on cell / gene clustering", "topics": [ "factorizeMatrix", "factorizeMatrix,ANY,celda_C-method", "factorizeMatrix,ANY,celda_CG-method", "factorizeMatrix,ANY,celda_G-method", "factorizeMatrix,SingleCellExperiment,ANY-method" ] }, { "page": "fastNormProp", "title": "Fast normalization for numeric matrix", "topics": [ "fastNormProp" ] }, { "page": "fastNormPropLog", "title": "Fast normalization for numeric matrix", "topics": [ "fastNormPropLog" ] }, { "page": "fastNormPropSqrt", "title": "Fast normalization for numeric matrix", "topics": [ "fastNormPropSqrt" ] }, { "page": "featureModuleLookup", "title": "Obtain the gene module of a gene of interest", "topics": [ "featureModuleLookup", "featureModuleLookup,SingleCellExperiment-method" ] }, { "page": "featureModuleTable", "title": "Output a feature module table", "topics": [ "featureModuleTable" ] }, { "page": "findMarkersTree", "title": "Generate marker decision tree from single-cell clustering output", "topics": [ "findMarkersTree" ] }, { "page": "geneSetEnrich", "title": "Gene set enrichment", "topics": [ "geneSetEnrich", "geneSetEnrich,matrix-method", "geneSetEnrich,SingleCellExperiment-method" ] }, { "page": "getDecisions", "title": "Gets cluster estimates using rules generated by `celda::findMarkersTree`", "topics": [ "getDecisions" ] }, { "page": "logLikelihood", "title": "Calculate the Log-likelihood of a celda model", "topics": [ "logLikelihood", "logLikelihood,matrix,celda_C-method", "logLikelihood,matrix,celda_CG-method", "logLikelihood,matrix,celda_G-method", "logLikelihood,SingleCellExperiment,ANY-method" ] }, { "page": "logLikelihoodHistory", "title": "Get log-likelihood history", "topics": [ "logLikelihoodHistory", "logLikelihoodHistory,celdaModel-method", "logLikelihoodHistory,SingleCellExperiment-method" ] }, { "page": "matrixNames", "title": "Get feature, cell and sample names from a celdaModel", "topics": [ "matrixNames", "matrixNames,celdaModel-method" ] }, { "page": "moduleHeatmap", "title": "Heatmap for featureModules", "topics": [ "moduleHeatmap", "moduleHeatmap,SingleCellExperiment-method" ] }, { "page": "nonzero", "title": "get row and column indices of none zero elements in the matrix", "topics": [ "nonzero" ] }, { "page": "normalizeCounts", "title": "Normalization of count data", "topics": [ "normalizeCounts" ] }, { "page": "params", "title": "Get parameter values provided for celdaModel creation", "topics": [ "params", "params,celdaModel-method" ] }, { "page": "perplexity", "title": "Calculate the perplexity of a celda model", "topics": [ "perplexity", "perplexity,ANY,celda_C-method", "perplexity,ANY,celda_CG-method", "perplexity,ANY,celda_G-method", "perplexity,SingleCellExperiment,ANY-method" ] }, { "page": "plotCeldaViolin", "title": "Feature Expression Violin Plot", "topics": [ "plotCeldaViolin", "plotCeldaViolin,ANY-method", "plotCeldaViolin,SingleCellExperiment-method" ] }, { "page": "plotDecontXContamination", "title": "Plots contamination on UMAP coordinates", "topics": [ "plotDecontXContamination" ] }, { "page": "plotDecontXMarkerExpression", "title": "Plots expression of marker genes before and after decontamination", "topics": [ "plotDecontXMarkerExpression" ] }, { "page": "plotDecontXMarkerPercentage", "title": "Plots percentage of cells cell types expressing markers", "topics": [ "plotDecontXMarkerPercentage" ] }, { "page": "plotDendro", "title": "Plots dendrogram of _findMarkersTree_ output", "topics": [ "plotDendro" ] }, { "page": "plotDimReduceCluster", "title": "Plotting the cell labels on a dimension reduction plot", "topics": [ "plotDimReduceCluster", "plotDimReduceCluster,SingleCellExperiment-method", "plotDimReduceCluster,vector-method" ] }, { "page": "plotDimReduceFeature", "title": "Plotting feature expression on a dimension reduction plot", "topics": [ "plotDimReduceFeature", "plotDimReduceFeature,ANY-method", "plotDimReduceFeature,SingleCellExperiment-method" ] }, { "page": "plotDimReduceGrid", "title": "Mapping the dimension reduction plot", "topics": [ "plotDimReduceGrid", "plotDimReduceGrid,ANY-method", "plotDimReduceGrid,SingleCellExperiment-method" ] }, { "page": "plotDimReduceModule", "title": "Plotting Celda module probability on a dimension reduction plot", "topics": [ "plotDimReduceModule", "plotDimReduceModule,ANY-method", "plotDimReduceModule,SingleCellExperiment-method" ] }, { "page": "plotGridSearchPerplexity", "title": "Visualize perplexity of a list of celda models", "topics": [ "plotGridSearchPerplexity", "plotGridSearchPerplexity,celdaList-method", "plotGridSearchPerplexity,SingleCellExperiment-method" ] }, { "page": "plotHeatmap", "title": "Plots heatmap based on Celda model", "topics": [ "plotHeatmap" ] }, { "page": "plotMarkerHeatmap", "title": "Generate heatmap for a marker decision tree", "topics": [ "plotMarkerHeatmap" ] }, { "page": "plotRPC", "title": "Visualize perplexity differences of a list of celda models", "topics": [ "plotRPC", "plotRPC,celdaList-method", "plotRPC,SingleCellExperiment-method" ] }, { "page": "recodeClusterY", "title": "Recode feature module labels", "topics": [ "recodeClusterY" ] }, { "page": "recodeClusterZ", "title": "Recode cell cluster labels", "topics": [ "recodeClusterZ" ] }, { "page": "recursiveSplitCell", "title": "Recursive cell splitting", "topics": [ "recursiveSplitCell", "recursiveSplitCell,matrix-method", 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