appendCeldaList         Append two celdaList objects
availableModels         available models
bestLogLikelihood       Get the log-likelihood
bestLogLikelihood,celdaModel-method
                        Get the log-likelihood
celda                   Celda models
celdaCGGridSearchRes    celdaCGGridSearchRes
celdaCGMod              celdaCGmod
celdaCGSim              celdaCGSim
celdaCMod               celdaCMod
celdaCSim               celdaCSim
celdaGMod               celdaGMod
celdaGSim               celdaGSim
celdaGridSearch         Run Celda in parallel with multiple parameters
celdaHeatmap            Plot celda Heatmap
celdaHeatmap,celda_C-method
                        Heatmap for celda_C
celdaHeatmap,celda_CG-method
                        Heatmap for celda_CG
celdaHeatmap,celda_G-method
                        Heatmap for celda_CG
celdaPerplexity         Get perplexity for every model in a celdaList
celdaPerplexity,celdaList-method
                        Get perplexity for every model in a celdaList
celdaProbabilityMap     Renders probability and relative expression
                        heatmaps to visualize the relationship between
                        feature modules and cell populations.
celdaProbabilityMap,celda_C-method
                        Probability map for a celda_C model
celdaProbabilityMap,celda_CG-method
                        Probability map for a celda_CG model
celdaTsne               Embeds cells in two dimensions using tSNE based
                        on celda_CG results.
celdaTsne,celda_C-method
                        tSNE for celda_C
celdaTsne,celda_CG-method
                        tSNE for celda_CG
celdaTsne,celda_G-method
                        tSNE for celda_G
celdaUmap               Embeds cells in two dimensions using umap.
celdaUmap,celda_C-method
                        umap for celda_C
celdaUmap,celda_CG-method
                        umap for celda_CG
celdaUmap,celda_G-method
                        umap for celda_G
celda_C                 Cell clustering with Celda
celda_CG                Cell and feature clustering with Celda
celda_G                 Feature clustering with Celda
clusterProbability      Get cluster probability
clusterProbability,celda_C-method
                        Conditional probabilities for cells in
                        subpopulations from a Celda_C model
clusterProbability,celda_CG-method
                        Conditional probabilities for cells and
                        features from a Celda_CG model
clusterProbability,celda_G-method
                        Conditional probabilities for features in
                        modules from a Celda_G model
clusters                Get clustering outcomes from a celdaModel
clusters,celdaModel-method
                        Get clustering outcomes from a celdaModel
compareCountMatrix      Check count matrix consistency
contaminationSim        contaminationSim
countChecksum           Get the MD5 hash of the count matrix from the
                        celdaList
countChecksum,celdaList-method
                        Get the MD5 hash of the count matrix from the
                        celdaList
decontX                 Contamination estimation with decontX
differentialExpression
                        Differential expression for cell subpopulations
                        using MAST
distinctColors          Create a color palette
eigenMatMultInt         Fast matrix multiplication for double x int
factorizeMatrix         Generate factorized matrices showing each
                        feature's influence on cell / gene clustering
factorizeMatrix,celda_C-method
                        Matrix factorization for results from celda_C()
factorizeMatrix,celda_CG-method
                        Matrix factorization for results from celda_CG
factorizeMatrix,celda_G-method
                        Matrix factorization for results from celda_G
fastNormProp            Fast normalization for numeric matrix
fastNormPropLog         Fast normalization for numeric matrix
fastNormPropSqrt        Fast normalization for numeric matrix
featureModuleLookup     Obtain the gene module of a gene of interest
featureModuleLookup,celda_C-method
                        Lookup the module of a feature
featureModuleLookup,celda_CG-method
                        Lookup the module of a feature
featureModuleLookup,celda_G-method
                        Lookup the module of a feature
featureModuleTable      Outputting a feature module table
findMarkers             Generate decision tree from single-cell
                        clustering output.
geneSetEnrich           Gene set enrichment
getDecisions            Gets cluster estimates using rules generated by
                        'celda::findMarkers'
logLikelihood           Calculate LogLikelihood
logLikelihoodHistory    Get log-likelihood history
logLikelihoodHistory,celdaModel-method
                        Get log-likelihood history
logLikelihoodcelda_C    Calculate Celda_C log likelihood
logLikelihoodcelda_CG   Calculate Celda_CG log likelihood
logLikelihoodcelda_G    Calculate Celda_G log likelihood
matrixNames             Get feature, cell and sample names from a
                        celdaModel
matrixNames,celdaModel-method
                        Get feature, cell and sample names from a
                        celdaModel
moduleHeatmap           Heatmap for featureModules
normalizeCounts         Normalization of count data
params                  Get parameter values provided for celdaModel
                        creation
params,celdaModel-method
                        Get parameter values provided for celdaModel
                        creation
perplexity              Calculate the perplexity from a single
                        celdaModel
perplexity,celda_C-method
                        Calculate the perplexity on new data with a
                        celda_C model
perplexity,celda_CG-method
                        Calculate the perplexity on new data with a
                        celda_CG model
perplexity,celda_G-method
                        Calculate the perplexity on new data with a
                        celda_G model
plotDendro              Plots dendrogram of 'findMarkers' output
plotDimReduceCluster    Plotting the cell labels on a dimensionality
                        reduction plot
plotDimReduceFeature    Plotting feature expression on a dimensionality
                        reduction plot
plotDimReduceGrid       Mapping the dimensionality reduction plot
plotDimReduceModule     Plotting the Celda module probability on a
                        dimensionality reduction plot
plotGridSearchPerplexity
                        Visualize perplexity of a list of celda models
plotGridSearchPerplexitycelda_C
                        Plot perplexity as a function of K from celda_C
                        models
plotGridSearchPerplexitycelda_CG
                        Plot perplexity as a function of K and L from
                        celda_CG models
plotGridSearchPerplexitycelda_G
                        Plot perplexity as a function of L from a
                        celda_G model
plotHeatmap             Plots heatmap based on Celda model
recodeClusterY          Recode feature module clusters
recodeClusterZ          Recode cell cluster labels
recursiveSplitCell      Recursive cell splitting
recursiveSplitModule    Recursive module splitting
resList                 Get final celdaModels from a celdaList
resList,celdaList-method
                        Get final celdaModels from a celdaList
resamplePerplexity      Calculate and visualize perplexity of all
                        models in a celdaList, with count resampling
runParams               Get run parameters provided to
                        'celdaGridSearch()'
runParams,celdaList-method
                        Get run parameters provided to
                        'celdaGridSearch()'
sampleCells             sampleCells
sampleLabel             Get sampleLabels from a celdaModel
sampleLabel,celdaModel-method
                        Get sampleLabels from a celdaModel
selectBestModel         Select best chain within each combination of
                        parameters
semiPheatmap            A function to draw clustered heatmaps.
simulateCells           Simulate count data from the celda generative
                        models.
simulateCellscelda_C    Simulate cells from the celda_C model
simulateCellscelda_CG   Simulate cells from the celda_CG model
simulateCellscelda_G    Simulate cells from the celda_G model
simulateContaminatedMatrix
                        Simulate contaminated count matrix
subsetCeldaList         Subset celdaList object from celdaGridSearch
topRank                 Identify features with the highest influence on
                        clustering.
violinPlot              Feature Expression Violin Plot
