Man pages for compbiomed/celda
CEllular Latent Dirichlet Allocation
| available_models | available models |
| celda | Celda models |
| celda_C | Cell clustering with Celda |
| celda_CG | Cell and feature clustering with Celda |
| celda.CG.grid.search.res | celda.CG.grid.search.res |
| celda.CG.mod | celda.CG.mod |
| celda.CG.sim | celda.CG.sim |
| celda.C.mod | celda.C.mod |
| celda.C.sim | celda.C.sim |
| celda_G | Feature clustering with Celda |
| celda.G.mod | celda.G.mod |
| celdaGridSearch | Run Celda in parallel with multiple parameters |
| celda.G.sim | celda.G.sim |
| celdaHeatmap | Render a stylable heatmap of count data based on celda... |
| celdaHeatmap.celda_C | Heatmap for celda_C |
| celdaHeatmap.celda_CG | Heatmap for celda_CG |
| celdaHeatmap.celda_G | Heatmap for celda_CG |
| celdaProbabilityMap | Renders probability and relative expression heatmaps to... |
| celdaProbabilityMap.celda_C | Probability map for a celda_C model |
| celdaProbabilityMap.celda_CG | Probability map for a celda_CG model |
| celdaTsne | Embeds cells in two dimensions using tSNE based on celda_CG... |
| celdaTsne.celda_C | tSNE for celda_C |
| celdaTsne.celda_CG | tSNE for celda_CG |
| celdaTsne.celda_G | tSNE for celda_G |
| clusterProbability | Get the probability of the cluster assignments generated... |
| clusterProbability.celda_C | Conditional probabilities for cells in subpopulations from a... |
| clusterProbability.celda_CG | Conditional probabilities for cells and features from a... |
| clusterProbability.celda_G | Conditional probabilities for features in modules from a... |
| compareCountMatrix | Check count matrix consistency |
| completeLogLikelihood | Get the complete log likelihood for a given celda model. |
| contamination.sim | contamination.sim |
| DeconX | This function updates decontamination |
| differentialExpression | Differential expression for cell subpopulations using MAST |
| distinct_colors | Create a color palette |
| eigenMatMultInt | Fast matrix multiplication for double x int |
| factorizeMatrix | Generate factorized matrices showing each feature's influence... |
| factorizeMatrix.celda_C | Matrix factorization for results from celda_C() |
| factorizeMatrix.celda_CG | Matrix factorization for results from celda_CG |
| factorizeMatrix.celda_G | Matrix factorization for results from celda_G |
| 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 |
| featureModuleLookup.celda_C | Lookup the module of a feature |
| featureModuleLookup.celda_CG | Lookup the module of a feature |
| featureModuleLookup.celda_G | Lookup the module of a feature |
| featureModuleTable | Outputting a feature module table |
| finalLogLikelihood | Get the log likelihood from the final iteration of Gibbs... |
| logLikelihood | Calculate a log-likelihood for a user-provided cluster... |
| logLikelihood.celda_C | Calculate Celda_C log likelihood |
| logLikelihood.celda_CG | Calculate Celda_CG log likelihood |
| logLikelihood.celda_G | Calculate Celda_G log likelihood |
| moduleHeatmap | Heatmap for feature modules |
| normalizeCounts | Normalization of count data |
| perplexity | Calculate the perplexity from a single celda model |
| perplexity.celda_C | Calculate the perplexity on new data with a celda_C model |
| perplexity.celda_CG | Calculate the perplexity on new data with a celda_CG model |
| perplexity.celda_G | Calculate the perplexity on new data with a celda_G model |
| plotDimReduceCluster | Plotting the cell labels on a dimensionality reduction plot |
| plotDimReduceFeature | Plotting feature expression on a dimensionality reduction... |
| plotDimReduceGrid | Mapping the dimensionality reduction plot |
| plotDimReduceModule | Plotting the Celda module probability on a dimensionality... |
| plotGridSearchPerplexity | Visualize perplexity of every model in a celda_list, by... |
| plotGridSearchPerplexity.celda_C | Plot perplexity as a function of K from celda_C models |
| plotGridSearchPerplexity.celda_CG | Plot perplexity as a function of K and L from celda_CG models |
| plotGridSearchPerplexity.celda_G | Plot perplexity as a function of L from a celda_G model |
| plotHeatmap | Renders a heatmap based on a matrix of counts where rows are... |
| recodeClusterY | Recode feature module clusters |
| recodeClusterZ | Recode cell cluster labels |
| resamplePerplexity | Calculate and visualize perplexity of all models in a... |
| runParams | Get run parameters for a celda run. |
| sample.cells | sample.cells |
| selectBestModel | Select best chain within each combination of parameters |
| semi_pheatmap | A function to draw clustered heatmaps. |
| simulateCells | Simulate count data from the celda generative models. |
| simulateCells.celda_C | Simulate cells from the celda_C model |
| simulateCells.celda_CG | Simulate cells from the celda_CG model |
| simulateCells.celda_G | Simulate cells from the celda_G model |
| simulateObservedMatrix | This function generates a list containing two count matrices... |
| subsetCeldaList | Subset celda_list object from celdaGridSearch |
| topRank | Identify features with the highest influence on clustering. |
| violinPlot | Feature Expression Violin Plot |
