Man pages for celda
CEllular Latent Dirichlet Allocation
| appendCeldaList | Append two celdaList objects |
| availableModels | available models |
| bestLogLikelihood | Get the log-likelihood |
| celda | Celda models |
| celda_C | Cell clustering with Celda |
| celda_CG | Cell and feature clustering with Celda |
| celdaCGGridSearchRes | celdaCGGridSearchRes |
| celdaCGMod | celdaCGmod |
| celdaCGSim | celdaCGSim |
| celdaClusters | Get or set the cell cluster labels from a celda... |
| celdaCMod | celdaCMod |
| celdaCSim | celdaCSim |
| celda_G | Feature clustering with Celda |
| celdaGMod | celdaGMod |
| celdaGridSearch | Run Celda in parallel with multiple parameters |
| celdaGSim | celdaGSim |
| celdaHeatmap | Plot celda Heatmap |
| celdaModel | Get celda model from a celda SingleCellExperiment object |
| celdaModules | Get or set the feature module labels from a celda... |
| celdaPerplexity | Get perplexity for every model in a celdaList |
| celdaPerplexity-celdaList-method | Get perplexity for every model in a celdaList |
| celdaProbabilityMap | Probability map for a celda model |
| celdatosce | Convert old celda model object to 'SCE' object |
| celdaTsne | t-Distributed Stochastic Neighbor Embedding (t-SNE) dimension... |
| celdaUmap | Uniform Manifold Approximation and Projection (UMAP)... |
| clusterProbability | Get the conditional probabilities of cell in subpopulations... |
| compareCountMatrix | Check count matrix consistency |
| contaminationSim | contaminationSim |
| countChecksum | Get the MD5 hash of the count matrix from the celdaList |
| countChecksum-celdaList-method | Get the MD5 hash of the count matrix from the celdaList |
| decontX | Contamination estimation with decontX |
| decontXcounts | Get or set decontaminated counts matrix |
| differentialExpression | Differential expression for cell subpopulations using MAST |
| distinctColors | Create a color palette |
| eigenMatMultInt | Fast matrix multiplication for double x int |
| factorizeMatrix | Generate factorized matrices showing each feature's influence... |
| 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 |
| featureModuleTable | Output a feature module table |
| findMarkersTree | Generate marker decision tree from single-cell clustering... |
| geneSetEnrich | Gene set enrichment |
| getDecisions | Gets cluster estimates using rules generated by... |
| logLikelihood | Calculate the Log-likelihood of a celda model |
| logLikelihoodHistory | Get log-likelihood history |
| matrixNames | Get feature, cell and sample names from a celdaModel |
| moduleHeatmap | Heatmap for featureModules |
| nonzero | get row and column indices of none zero elements in the... |
| normalizeCounts | Normalization of count data |
| params | Get parameter values provided for celdaModel creation |
| perplexity | Calculate the perplexity of a celda model |
| plotCeldaViolin | Feature Expression Violin Plot |
| plotDecontXContamination | Plots contamination on UMAP coordinates |
| plotDecontXMarkerExpression | Plots expression of marker genes before and after... |
| plotDecontXMarkerPercentage | Plots percentage of cells cell types expressing markers |
| plotDimReduceCluster | Plotting the cell labels on a dimension reduction plot |
| plotDimReduceFeature | Plotting feature expression on a dimension reduction plot |
| plotDimReduceGrid | Mapping the dimension reduction plot |
| plotDimReduceModule | Plotting Celda module probability on a dimension reduction... |
| plotGridSearchPerplexity | Visualize perplexity of a list of celda models |
| plotGridSearchPerplexityDiff | Visualize perplexity differences of a list of celda models |
| plotHeatmap | Plots heatmap based on Celda model |
| plotMarkerDendro | Plots dendrogram of _findMarkersTree_ output |
| plotMarkerHeatmap | Generate heatmap for a marker decision tree |
| recodeClusterY | Recode feature module labels |
| recodeClusterZ | Recode cell cluster labels |
| recursiveSplitCell | Recursive cell splitting |
| recursiveSplitModule | Recursive module splitting |
| resamplePerplexity | Calculate and visualize perplexity of all models in a... |
| resList | Get final celdaModels from a celda model 'SCE' or celdaList... |
| retrieveFeatureIndex | Retrieve row index for a set of features |
| runParams | Get run parameters from a celda model 'SingleCellExperiment'... |
| sampleCells | sampleCells |
| sampleLabel | Get or set sample labels from a celda SingleCellExperiment... |
| sceCeldaC | sceCeldaC |
| sceCeldaCG | sceCeldaCG |
| sceCeldaCGGridSearch | sceCeldaCGGridSearch |
| sceCeldaG | sceCeldaG |
| selectBestModel | Select best chain within each combination of parameters |
| selectFeatures | Simple feature selection by feature counts |
| semiPheatmap | A function to draw clustered heatmaps. |
| simulateCells | Simulate count data from the celda generative models. |
| simulateContamination | Simulate contaminated count matrix |
| splitModule | Split celda feature module |
| subsetCeldaList | Subset celda model from SCE object returned from... |
| topRank | Identify features with the highest influence on clustering. |
