Man pages for compbiomed/celda
CEllular Latent Dirichlet Allocation

available_modelsavailable models
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
celdaHeatmapRender a stylable heatmap of count data based on celda...
celdaHeatmap.celda_CHeatmap for celda_C
celdaHeatmap.celda_CGHeatmap for celda_CG
celdaHeatmap.celda_GHeatmap for celda_CG
celdaProbabilityMapRenders probability and relative expression heatmaps to...
celdaProbabilityMap.celda_CProbability map for a celda_C model
celdaProbabilityMap.celda_CGProbability map for a celda_CG model
celdaTsneEmbeds cells in two dimensions using tSNE based on celda_CG...
celdaTsne.celda_CtSNE for celda_C
celdaTsne.celda_CGtSNE for celda_CG
celdaTsne.celda_GtSNE for celda_G
clusterProbabilityGet the probability of the cluster assignments generated...
clusterProbability.celda_CConditional probabilities for cells in subpopulations from a...
clusterProbability.celda_CGConditional probabilities for cells and features from a...
clusterProbability.celda_GConditional probabilities for features in modules from a...
compareCountMatrixCheck count matrix consistency
completeLogLikelihoodGet the complete log likelihood for a given celda model.
DeconXThis function updates decontamination
differentialExpressionDifferential expression for cell subpopulations using MAST
distinct_colorsCreate a color palette
eigenMatMultIntFast matrix multiplication for double x int
factorizeMatrixGenerate factorized matrices showing each feature's influence...
factorizeMatrix.celda_CMatrix factorization for results from celda_C()
factorizeMatrix.celda_CGMatrix factorization for results from celda_CG
factorizeMatrix.celda_GMatrix 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_CLookup the module of a feature
featureModuleLookup.celda_CGLookup the module of a feature
featureModuleLookup.celda_GLookup the module of a feature
featureModuleTableOutputting a feature module table
finalLogLikelihoodGet the log likelihood from the final iteration of Gibbs...
logLikelihoodCalculate a log-likelihood for a user-provided cluster...
logLikelihood.celda_CCalculate Celda_C log likelihood
logLikelihood.celda_CGCalculate Celda_CG log likelihood
logLikelihood.celda_GCalculate Celda_G log likelihood
moduleHeatmapHeatmap for feature modules
normalizeCountsNormalization of count data
perplexityCalculate the perplexity from a single celda model
perplexity.celda_CCalculate the perplexity on new data with a celda_C model
perplexity.celda_CGCalculate the perplexity on new data with a celda_CG model
perplexity.celda_GCalculate the perplexity on new data with a celda_G model
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 every model in a celda_list, by...
plotGridSearchPerplexity.celda_CPlot perplexity as a function of K from celda_C models
plotGridSearchPerplexity.celda_CGPlot perplexity as a function of K and L from celda_CG models
plotGridSearchPerplexity.celda_GPlot perplexity as a function of L from a celda_G model
plotHeatmapRenders a heatmap based on a matrix of counts where rows are...
recodeClusterYRecode feature module clusters
recodeClusterZRecode cell cluster labels
resamplePerplexityCalculate and visualize perplexity of all models in a...
runParamsGet run parameters for a celda run.
selectBestModelSelect best chain within each combination of parameters
semi_pheatmapA function to draw clustered heatmaps.
simulateCellsSimulate count data from the celda generative models.
simulateCells.celda_CSimulate cells from the celda_C model
simulateCells.celda_CGSimulate cells from the celda_CG model
simulateCells.celda_GSimulate cells from the celda_G model
simulateObservedMatrixThis function generates a list containing two count matrices...
subsetCeldaListSubset celda_list object from celdaGridSearch
topRankIdentify features with the highest influence on clustering.
violinPlotFeature Expression Violin Plot
compbiomed/celda documentation built on May 25, 2019, 3:58 a.m.