Man pages for celda
CEllular Latent Dirichlet Allocation

appendCeldaListAppend two celdaList objects
availableModelsavailable models
bestLogLikelihoodGet the log-likelihood
celdaCelda models
celda_CCell clustering with Celda
celda_CGCell and feature clustering with Celda
celdaClustersGet or set the cell cluster labels from a celda...
celda_GFeature clustering with Celda
celdaGridSearchRun Celda in parallel with multiple parameters
celdaHeatmapPlot celda Heatmap
celdaModelGet celda model from a celda SingleCellExperiment object
celdaModulesGet or set the feature module labels from a celda...
celdaPerplexityGet perplexity for every model in a celdaList
celdaPerplexity-celdaList-methodGet perplexity for every model in a celdaList
celdaProbabilityMapProbability map for a celda model
celdatosceConvert old celda model object to 'SCE' object
celdaTsnet-Distributed Stochastic Neighbor Embedding (t-SNE) dimension...
celdaUmapUniform Manifold Approximation and Projection (UMAP)...
clusterProbabilityGet the conditional probabilities of cell in subpopulations...
compareCountMatrixCheck count matrix consistency
countChecksumGet the MD5 hash of the count matrix from the celdaList
countChecksum-celdaList-methodGet the MD5 hash of the count matrix from the celdaList
decontXContamination estimation with decontX
decontXcountsGet or set decontaminated counts matrix
differentialExpressionDifferential expression for cell subpopulations using MAST
distinctColorsCreate a color palette
eigenMatMultIntFast matrix multiplication for double x int
factorizeMatrixGenerate factorized matrices showing each feature's influence...
fastNormPropFast normalization for numeric matrix
fastNormPropLogFast normalization for numeric matrix
fastNormPropSqrtFast normalization for numeric matrix
featureModuleLookupObtain the gene module of a gene of interest
featureModuleTableOutput a feature module table
findMarkersTreeGenerate marker decision tree from single-cell clustering...
geneSetEnrichGene set enrichment
getDecisionsGets cluster estimates using rules generated by...
logLikelihoodCalculate the Log-likelihood of a celda model
logLikelihoodHistoryGet log-likelihood history
matrixNamesGet feature, cell and sample names from a celdaModel
moduleHeatmapHeatmap for featureModules
nonzeroget row and column indices of none zero elements in the...
normalizeCountsNormalization of count data
paramsGet parameter values provided for celdaModel creation
perplexityCalculate the perplexity of a celda model
plotCeldaViolinFeature Expression Violin Plot
plotDecontXContaminationPlots contamination on UMAP coordinates
plotDecontXMarkerExpressionPlots expression of marker genes before and after...
plotDecontXMarkerPercentagePlots percentage of cells cell types expressing markers
plotDimReduceClusterPlotting the cell labels on a dimension reduction plot
plotDimReduceFeaturePlotting feature expression on a dimension reduction plot
plotDimReduceGridMapping the dimension reduction plot
plotDimReduceModulePlotting Celda module probability on a dimension reduction...
plotGridSearchPerplexityVisualize perplexity of a list of celda models
plotGridSearchPerplexityDiffVisualize perplexity differences of a list of celda models
plotHeatmapPlots heatmap based on Celda model
plotMarkerDendroPlots dendrogram of _findMarkersTree_ output
plotMarkerHeatmapGenerate heatmap for a marker decision tree
recodeClusterYRecode feature module labels
recodeClusterZRecode cell cluster labels
recursiveSplitCellRecursive cell splitting
recursiveSplitModuleRecursive module splitting
resamplePerplexityCalculate and visualize perplexity of all models in a...
resListGet final celdaModels from a celda model 'SCE' or celdaList...
retrieveFeatureIndexRetrieve row index for a set of features
runParamsGet run parameters from a celda model 'SingleCellExperiment'...
sampleLabelGet or set sample labels from a celda SingleCellExperiment...
selectBestModelSelect best chain within each combination of parameters
selectFeaturesSimple feature selection by feature counts
semiPheatmapA function to draw clustered heatmaps.
simulateCellsSimulate count data from the celda generative models.
simulateContaminationSimulate contaminated count matrix
splitModuleSplit celda feature module
subsetCeldaListSubset celda model from SCE object returned from...
topRankIdentify features with the highest influence on clustering.
celda documentation built on Nov. 8, 2020, 8:24 p.m.