Man pages for celda
CEllular Latent Dirichlet Allocation

appendCeldaListAppend two celdaList objects
availableModelsavailable models
bestLogLikelihoodGet the log-likelihood
bestLogLikelihood-celdaModel-methodGet the log-likelihood
celdaCelda models
celda_CCell clustering with Celda
celda_CGCell and feature clustering with Celda
celda_GFeature clustering with Celda
celdaGridSearchRun Celda in parallel with multiple parameters
celdaHeatmapPlot celda Heatmap
celdaHeatmap-celda_CG-methodHeatmap for celda_CG
celdaHeatmap-celda_C-methodHeatmap for celda_C
celdaHeatmap-celda_G-methodHeatmap for celda_CG
celdaPerplexityGet perplexity for every model in a celdaList
celdaPerplexity-celdaList-methodGet perplexity for every model in a celdaList
celdaProbabilityMapRenders probability and relative expression heatmaps to...
celdaProbabilityMap-celda_CG-methodProbability map for a celda_CG model
celdaProbabilityMap-celda_C-methodProbability map for a celda_C model
celdaTsneEmbeds cells in two dimensions using tSNE based on celda_CG...
celdaTsne-celda_CG-methodtSNE for celda_CG
celdaTsne-celda_C-methodtSNE for celda_C
celdaTsne-celda_G-methodtSNE for celda_G
celdaUmapEmbeds cells in two dimensions using umap.
celdaUmap-celda_CG-methodumap for celda_CG
celdaUmap-celda_C-methodumap for celda_C
celdaUmap-celda_G-methodumap for celda_G
clusterProbabilityGet cluster probability
clusterProbability-celda_CG-methodConditional probabilities for cells and features from a...
clusterProbability-celda_C-methodConditional probabilities for cells in subpopulations from a...
clusterProbability-celda_G-methodConditional probabilities for features in modules from a...
clustersGet clustering outcomes from a celdaModel
clusters-celdaModel-methodGet clustering outcomes from a celdaModel
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...
factorizeMatrix-celda_CG-methodMatrix factorization for results from celda_CG
factorizeMatrix-celda_C-methodMatrix factorization for results from celda_C()
factorizeMatrix-celda_G-methodMatrix factorization for results from celda_G
fastNormPropFast normalization for numeric matrix
fastNormPropLogFast normalization for numeric matrix
fastNormPropSqrtFast normalization for numeric matrix
featureModuleLookupObtain the gene module of a gene of interest
featureModuleLookup-celda_CG-methodLookup the module of a feature
featureModuleLookup-celda_C-methodLookup the module of a feature
featureModuleLookup-celda_G-methodLookup the module of a feature
featureModuleTableOutputting a feature module table
findMarkersTreeGenerate marker decision tree from single-cell clustering...
geneSetEnrichGene set enrichment
getDecisionsGets cluster estimates using rules generated by...
logLikelihoodCalculate LogLikelihood
logLikelihoodcelda_CCalculate Celda_C log likelihood
logLikelihoodcelda_CGCalculate Celda_CG log likelihood
logLikelihoodcelda_GCalculate Celda_G log likelihood
logLikelihoodHistoryGet log-likelihood history
logLikelihoodHistory-celdaModel-methodGet log-likelihood history
matrixNamesGet feature, cell and sample names from a celdaModel
matrixNames-celdaModel-methodGet 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
params-celdaModel-methodGet parameter values provided for celdaModel creation
perplexityCalculate the perplexity from a single celdaModel
perplexity-celda_CG-methodCalculate the perplexity on new data with a celda_CG model
perplexity-celda_C-methodCalculate the perplexity on new data with a celda_C model
perplexity-celda_G-methodCalculate the perplexity on new data with a celda_G 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 dimensionality reduction plot
plotDimReduceFeaturePlotting feature expression on a dimensionality reduction...
plotDimReduceGridMapping the dimensionality reduction plot
plotDimReduceModulePlotting the Celda module probability on a dimensionality...
plotGridSearchPerplexityVisualize perplexity of a list of celda models
plotGridSearchPerplexitycelda_CPlot perplexity as a function of K from celda_C models
plotGridSearchPerplexitycelda_CGPlot perplexity as a function of K and L from celda_CG models
plotGridSearchPerplexitycelda_GPlot perplexity as a function of L from a celda_G model
plotHeatmapPlots heatmap based on Celda model
plotMarkerDendroPlots dendrogram of _findMarkersTree_ output
plotMarkerHeatmapGenerate heatmap for a marker decision tree
recodeClusterYRecode feature module clusters
recodeClusterZRecode cell cluster labels
recursiveSplitCellRecursive cell splitting
recursiveSplitModuleRecursive module splitting
resamplePerplexityCalculate and visualize perplexity of all models in a...
resListGet final celdaModels from a celdaList
resList-celdaList-methodGet final celdaModels from a celdaList
retrieveFeatureIndexRetrieve row index for a set of features
runParamsGet run parameters provided to 'celdaGridSearch()'
runParams-celdaList-methodGet run parameters provided to 'celdaGridSearch()'
sampleLabelGet sampleLabels from a celdaModel
sampleLabel-celdaModel-methodGet sampleLabels from a celdaModel
selectBestModelSelect best chain within each combination of parameters
semiPheatmapA function to draw clustered heatmaps.
simulateCellsSimulate count data from the celda generative models.
simulateCellscelda_CSimulate cells from the celda_C model
simulateCellscelda_CGSimulate cells from the celda_CG model
simulateCellscelda_GSimulate cells from the celda_G model
simulateContaminationSimulate contaminated count matrix
subsetCeldaListSubset celdaList object from celdaGridSearch
topRankIdentify features with the highest influence on clustering.
celda documentation built on June 9, 2020, 2 a.m.