Primary celda functionsFunctions for clustering of cells |
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Cell and feature clustering with Celda |
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Cell clustering with Celda |
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Feature clustering with Celda |
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Generate an HTML report for celda_CG |
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Simple feature selection by feature counts |
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Split celda feature module |
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Visualization functions for celda resultsFunctions for displaying celda resuls on 2-D embeddings, heatmaps, and violin plots |
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Uniform Manifold Approximation and Projection (UMAP) dimension
reduction for celda |
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t-Distributed Stochastic Neighbor Embedding (t-SNE) dimension
reduction for celda |
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Heatmap for featureModules |
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Probability map for a celda model |
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Plotting the cell labels on a dimension reduction plot |
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Plotting feature expression on a dimension reduction plot |
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Plotting Celda module probability on a dimension reduction plot |
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Mapping the dimension reduction plot |
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Feature Expression Violin Plot |
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Plot celda Heatmap |
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Primary decontX functionsFunctions for estimating and displaying contamination with decontX |
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Contamination estimation with decontX |
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Plots contamination on UMAP coordinates |
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Plots expression of marker genes before and after decontamination |
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Plots percentage of cells cell types expressing markers |
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Get or set decontaminated counts matrix |
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Functions for determining the numbers of clusters in celdaFunctions for running and comparing multiple celda models with different number of modules or cell populations |
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Recursive cell splitting |
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Recursive module splitting |
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Visualize perplexity differences of a list of celda models |
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Run Celda in parallel with multiple parameters |
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Visualize perplexity of a list of celda models |
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Calculate the perplexity of a celda model |
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Calculate and visualize perplexity of all models in a celdaList |
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Select best chain within each combination of parameters |
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Get final celdaModels from a celda model |
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Subset celda model from SCE object returned from
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Append two celdaList objects |
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Get perplexity for every model in a celdaList |
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Miscellaneous celda functionsVarious functions for manipulation of celda results |
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Get or set the cell cluster labels from a celda SingleCellExperiment object or celda model object. |
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Get or set the feature module labels from a celda SingleCellExperiment object. |
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Recode feature module labels |
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Recode cell cluster labels |
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Reorder cells populations and/or features modules using hierarchical clustering |
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Obtain the gene module of a gene of interest |
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Output a feature module table |
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Celda models |
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Get parameter values provided for celdaModel creation |
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Get run parameters from a celda model
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Generate factorized matrices showing each feature's influence on cell / gene clustering |
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Get the log-likelihood |
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Get the conditional probabilities of cell in subpopulations from celda model |
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Gene set enrichment |
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Plots heatmap based on Celda model |
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Retrieve row index for a set of features |
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Normalization of count data |
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Create a color palette |
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Get feature, cell and sample names from a celdaModel |
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Calculate the Log-likelihood of a celda model |
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Get log-likelihood history |
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Identify features with the highest influence on clustering. |
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Get or set sample labels from a celda SingleCellExperiment object |
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Simulation functionsFunctions for generating data from the generative process of each model |
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Simulate count data from the celda generative models. |
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Simulate contaminated count matrix |
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Data objectsSmall data objects used in examples |
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sceCeldaCG |
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sceCeldaC |
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sceCeldaG |
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sceCeldaCGGridSearch |
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celdaCGGridSearchRes |
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sampleCells |
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contaminationSim |