appendCeldaList         Append two celdaList objects
availableModels         available models
bestLogLikelihood       Get the log-likelihood
celda                   Celda models
celda_C                 Cell clustering with Celda
celda_CG                Cell and feature clustering with Celda
celda_G                 Feature clustering with Celda
celdaCGGridSearchRes    celdaCGGridSearchRes
celdaCGMod              celdaCGmod
celdaCGSim              celdaCGSim
celdaClusters           Get or set the cell cluster labels from a celda
                        SingleCellExperiment object or celda model
                        object.
celdaCMod               celdaCMod
celdaCSim               celdaCSim
celdaGMod               celdaGMod
celdaGridSearch         Run Celda in parallel with multiple parameters
celdaGSim               celdaGSim
celdaHeatmap            Plot celda Heatmap
celdaModel              Get celda model from a celda
                        SingleCellExperiment object
celdaModules            Get or set the feature module labels from a
                        celda SingleCellExperiment object.
celdaPerplexity         Get perplexity for every model in a celdaList
celdaPerplexity,celdaList-method
                        Get perplexity for every model in a celdaList
celdaProbabilityMap     Probability map for a celda model
celdatosce              Convert old celda model object to 'SCE' object
celdaTsne               t-Distributed Stochastic Neighbor Embedding
                        (t-SNE) dimension reduction for celda 'sce'
                        object
celdaUmap               Uniform Manifold Approximation and Projection
                        (UMAP) dimension reduction for celda 'sce'
                        object
clusterProbability      Get the conditional probabilities of cell in
                        subpopulations from celda model
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
decontXcounts           Get or set decontaminated counts matrix
distinctColors          Create a color palette
eigenMatMultInt         Fast matrix multiplication for double x int
eigenMatMultNumeric     Fast matrix multiplication for double x double
factorizeMatrix         Generate factorized matrices showing each
                        feature's influence on cell / gene clustering
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
featureModuleTable      Output a feature module table
findMarkersTree         Generate marker decision tree from single-cell
                        clustering output
geneSetEnrich           Gene set enrichment
getDecisions            Gets cluster estimates using rules generated by
                        'celda::findMarkersTree'
logLikelihood           Calculate the Log-likelihood of a celda model
logLikelihoodHistory    Get log-likelihood history
matrixNames             Get feature, cell and sample names from a
                        celdaModel
moduleHeatmap           Heatmap for featureModules
nonzero                 get row and column indices of none zero
                        elements in the matrix
normalizeCounts         Normalization of count data
params                  Get parameter values provided for celdaModel
                        creation
perplexity              Calculate the perplexity of a celda model
plotCeldaViolin         Feature Expression Violin Plot
plotDecontXContamination
                        Plots contamination on UMAP coordinates
plotDecontXMarkerExpression
                        Plots expression of marker genes before and
                        after decontamination
plotDecontXMarkerPercentage
                        Plots percentage of cells cell types expressing
                        markers
plotDendro              Plots dendrogram of _findMarkersTree_ output
plotDimReduceCluster    Plotting the cell labels on a dimension
                        reduction plot
plotDimReduceFeature    Plotting feature expression on a dimension
                        reduction plot
plotDimReduceGrid       Mapping the dimension reduction plot
plotDimReduceModule     Plotting Celda module probability on a
                        dimension reduction plot
plotGridSearchPerplexity
                        Visualize perplexity of a list of celda models
plotHeatmap             Plots heatmap based on Celda model
plotMarkerHeatmap       Generate heatmap for a marker decision tree
plotRPC                 Visualize perplexity differences of a list of
                        celda models
recodeClusterY          Recode feature module labels
recodeClusterZ          Recode cell cluster labels
recursiveSplitCell      Recursive cell splitting
recursiveSplitModule    Recursive module splitting
reorderCelda            Reorder cells populations and/or features
                        modules using hierarchical clustering
reportceldaCG           Generate an HTML report for celda_CG
resamplePerplexity      Calculate and visualize perplexity of all
                        models in a celdaList
resList                 Get final celdaModels from a celda model 'SCE'
                        or celdaList object
retrieveFeatureIndex    Retrieve row index for a set of features
runParams               Get run parameters from a celda model
                        'SingleCellExperiment' or 'celdaList' object
sampleCells             sampleCells
sampleLabel             Get or set sample labels from a celda
                        SingleCellExperiment object
sceCeldaC               sceCeldaC
sceCeldaCG              sceCeldaCG
sceCeldaCGGridSearch    sceCeldaCGGridSearch
sceCeldaG               sceCeldaG
selectBestModel         Select best chain within each combination of
                        parameters
selectFeatures          Simple feature selection by feature counts
semiPheatmap            A function to draw clustered heatmaps.
simulateCells           Simulate count data from the celda generative
                        models.
simulateContamination   Simulate contaminated count matrix
splitModule             Split celda feature module
subsetCeldaList         Subset celda model from SCE object returned
                        from 'celdaGridSearch'
topRank                 Identify features with the highest influence on
                        clustering.
