Man pages for campbio/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
celdaCGGridSearchResceldaCGGridSearchRes
celdaCGModceldaCGmod
celdaCGSimceldaCGSim
celdaClustersGet or set the cell cluster labels from a celda...
celdaCModceldaCMod
celdaCSimceldaCSim
celda_GFeature clustering with Celda
celdaGModceldaGMod
celdaGridSearchRun Celda in parallel with multiple parameters
celdaGSimceldaGSim
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
contaminationSimcontaminationSim
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
distinctColorsCreate a color palette
eigenMatMultIntFast matrix multiplication for double x int
eigenMatMultNumericFast matrix multiplication for double x double
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
geneSetEnrichGene set enrichment
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
plotHeatmapPlots heatmap based on Celda model
plotRPCVisualize perplexity differences of a list of celda models
recodeClusterYRecode feature module labels
recodeClusterZRecode cell cluster labels
recursiveSplitCellRecursive cell splitting
recursiveSplitModuleRecursive module splitting
reorderCeldaReorder cells populations and/or features modules using...
reportceldaCGGenerate an HTML report for celda_CG
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'...
sampleCellssampleCells
sampleLabelGet or set sample labels from a celda SingleCellExperiment...
sceCeldaCsceCeldaC
sceCeldaCGsceCeldaCG
sceCeldaCGGridSearchsceCeldaCGGridSearch
sceCeldaGsceCeldaG
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.
campbio/celda documentation built on April 5, 2024, 11:47 a.m.