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"page": "comptsne", "title": "Computation of a two dimensional t-SNE representation", "topics": [ "comptsne" ] }, { "page": "compumap", "title": "Computation of a two dimensional umap representation", "topics": [ "compumap" ] }, { "page": "corrVar", "title": "Function for regressing out the mean-variance dependence. This function corrects for the systematic dependence of the variance on the mean by a local regression.", "topics": [ "corrVar" ] }, { "page": "createKnnMatrix", "title": "Function to create a knn matrix", "topics": [ "createKnnMatrix" ] }, { "page": "diffexpnb", "title": "Function for differential expression analysis", "topics": [ "diffexpnb" ] }, { "page": "diffgenes", "title": "Compute Expression Differences between Clusters", "topics": [ "diffgenes" ] }, { "page": "diffNoisyGenes", "title": "Function for extracting genes with elevated variability in a cluster", "topics": [ "diffNoisyGenes" ] }, { "page": "diffNoisyGenesTB", "title": "Function for extracting genes with differential biological variability in a cluster", "topics": [ "diffNoisyGenesTB" ] }, { "page": "extractCounts", "title": "Function for filtering count data", "topics": [ "extractCounts" ] }, { "page": "filterdata", "title": "Data filtering", "topics": [ "filterdata" ] }, { "page": "findoutliers", "title": "Inference 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"title": "Single-cell transcriptome data of intestinal epithelial cells", "topics": [ "intestinalData" ] }, { "page": "intestinalDataSmall", "title": "Single-cell transcriptome data of intestinal epithelial cells", "topics": [ "intestinalDataSmall" ] }, { "page": "lineagegraph", "title": "Inference of a Lineage Graph", "topics": [ "lineagegraph" ] }, { "page": "Ltree", "title": "The Ltree Class", "topics": [ "Ltree", "Ltree-class" ] }, { "page": "maxNoisyGenes", "title": "Function for extracting genes maximal variability", "topics": [ "maxNoisyGenes" ] }, { "page": "maxNoisyGenesTB", "title": "Function for extracting genes maximal variability", "topics": [ "maxNoisyGenesTB" ] }, { "page": "noiseBaseFit", "title": "Function for computing a fit to the baseline of gene expression variability", "topics": [ "noiseBaseFit" ] }, { "page": "plotB", "title": "Boxplots for features across clusters", "topics": [ "plotB" ] }, { "page": "plotbackground", "title": "Plot Background Model", "topics": [ "plotbackground" ] }, { "page": "plotBackVar", "title": "Function for plottinhg the background model of gene expression variability", "topics": [ "plotBackVar" ] }, { "page": "plotdiffgenes", "title": "Barplot of differentially expressed genes", "topics": [ "plotdiffgenes" ] }, { "page": "plotdiffgenesnb", "title": "Function for plotting differentially expressed genes", "topics": [ "plotdiffgenesnb" ] }, { "page": "plotDiffNoise", "title": "Function for plotting differentially variable genes", "topics": [ "plotDiffNoise" ] }, { "page": "plotdimsat", "title": "Plotting the Saturation of Explained Variance", "topics": [ "plotdimsat" ] }, { "page": "plotdistanceratio", "title": "Histogram of Cell-to-Cell Distances in Real versus Embedded Space", "topics": [ "plotdistanceratio" ] }, { "page": "plotexpmap", "title": "Highlighting gene expression in a dimensional reduction representation", "topics": [ "plotexpmap" ] }, { "page": "plotExpNoise", "title": "Noise-expression scatter plot", "topics": [ "plotExpNoise" ] }, { "page": "plotfeatmap", "title": "Highlighting feature values in a dimensional reduction representation", "topics": [ "plotfeatmap" ] }, { "page": "plotgraph", "title": "StemID2 Lineage Graph", "topics": [ "plotgraph" ] }, { "page": "plotjaccard", "title": "Plot Jaccard Similarities", "topics": [ "plotjaccard" ] }, { "page": "plotlabelsmap", "title": "Plot labels in a dimensional reduction representation", "topics": [ "plotlabelsmap" ] }, { "page": "plotlinkpv", "title": "Heatmap of Link P-values", "topics": [ "plotlinkpv" ] }, { "page": "plotlinkscore", "title": "Heatmap of Link Scores", "topics": [ "plotlinkscore" ] }, { "page": "plotmap", "title": "Plotting a dimensional reduction representation", "topics": [ "plotmap" ] }, { "page": "plotmarkergenes", "title": "Plotting a Heatmap of Marker Gene Expression", "topics": [ "plotmarkergenes" ] }, { "page": "plotMV", "title": "Plot of Mean-Variance dependence and various fits", "topics": [ "plotMV" ] }, { 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}, { "page": "plotRegNB", "title": "Function for plotting negative binomial regression", "topics": [ "plotRegNB" ] }, { "page": "plotsaturation", "title": "Plot Saturation of Within-Cluster Dispersion", "topics": [ "plotsaturation" ] }, { "page": "plotsensitivity", "title": "Plot Sensitivity", "topics": [ "plotsensitivity" ] }, { "page": "plotsilhouette", "title": "Plot Cluster Silhouette", "topics": [ "plotsilhouette" ] }, { "page": "plotspantree", "title": "Minimum Spanning Tree of RaceID3 clusters", "topics": [ "plotspantree" ] }, { "page": "plotsymbolsmap", "title": "Plotting groups as different symbols in a dimensional reduction representation", "topics": [ "plotsymbolsmap" ] }, { "page": "plotTrProbs", "title": "Function for plotting transition probabilities between clusters", "topics": [ "plotTrProbs" ] }, { "page": "plotUMINoise", "title": "Plotting noise dependence on total UMI count", "topics": [ "plotUMINoise" ] }, { "page": "postfntb", "title": "Posterior probability", 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