| barplotgene | Gene Expression Barplot |
| baseLineVar | Baseline gene expression variability |
| branchcells | Differential Gene Expression between Links |
| calcAlphaG | Function for calculating an aggregated dispersion parameter |
| calcVar | Function for calculating total variance from VarID fit |
| calcVarFit | Function for calculating the total variance fit |
| CCcorrect | Dimensional Reduction by PCA or ICA |
| cc_genes | Cell cycle markers for Mus Muscuus |
| cellsfromtree | Extract Cells on Differentiation Trajectory |
| cleanNN | Function for pruning k-nearest neighborhoods based on... |
| clustdiffgenes | Inference of differentially expressed genes in a cluster |
| clustexp | Clustering of single-cell transcriptome data |
| clustheatmap | Plotting a Heatmap of the Distance Matrix |
| compdist | Computing a distance matrix for cell type inference |
| compentropy | Compute transcriptome entropy of each cell |
| compfr | Computation of a two dimensional Fruchterman-Rheingold... |
| compMean | Function for computing local gene expression averages |
| compmedoids | Computes Medoids from a Clustering Partition |
| compNoise | Function for computing local gene expression variability |
| comppvalue | Computing P-values for Link Significance |
| compscore | Compute StemID2 score |
| compTBNoise | Function for fitting a negative binomial noise model of... |
| comptsne | Computation of a two dimensional t-SNE representation |
| compumap | Computation of a two dimensional umap representation |
| corrVar | Function for regressing out the mean-variance dependence.... |
| createKnnMatrix | Function to create a knn matrix |
| diffexpnb | Function for differential expression analysis |
| diffgenes | Compute Expression Differences between Clusters |
| diffNoisyGenes | Function for extracting genes with elevated variability in a... |
| diffNoisyGenesTB | Function for extracting genes with differential biological... |
| extractCounts | Function for filtering count data |
| filterdata | Data filtering |
| findoutliers | Inference of outlier cells and final clustering |
| fitBackVar | Function for computing a background model of gene expression... |
| fitGammaRt | Fitting a Gamma distribution to global cell-to-cell... |
| fitLogVarLogMean | Second order polynomial fit of mean-variance dependence This... |
| fitNBtb | Function for fitting a negative binomial noise model of... |
| fitNBtbCl | Function for fitting a negative binomial noise model of... |
| fractDotPlot | Dotplot of gene expression across clusters or samples |
| getExpData | Function for extracting a filtered expression matrix from a... |
| getfdata | Extracting filtered expression data |
| getFilteredCounts | Function for filtering count data |
| getNode | Extract all genes for a module in a FateID self-orgaizing map |
| getproj | Extract Projections of all Cells from a Cluster |
| graphCluster | Function for infering clustering of the pruned k nearest... |
| imputeexp | Imputed expression matrix |
| inspectKNN | Function for inspecting pruned k-nearest neighbourhoods |
| intestinalData | Single-cell transcriptome data of intestinal epithelial cells |
| intestinalDataSmall | Single-cell transcriptome data of intestinal epithelial cells |
| lineagegraph | Inference of a Lineage Graph |
| Ltree | The Ltree Class |
| maxNoisyGenes | Function for extracting genes maximal variability |
| maxNoisyGenesTB | Function for extracting genes maximal variability |
| noiseBaseFit | Function for computing a fit to the baseline of gene... |
| plotB | Boxplots for features across clusters |
| plotbackground | Plot Background Model |
| plotBackVar | Function for plottinhg the background model of gene... |
| plotdiffgenes | Barplot of differentially expressed genes |
| plotdiffgenesnb | Function for plotting differentially expressed genes |
| plotDiffNoise | Function for plotting differentially variable genes |
| plotdimsat | Plotting the Saturation of Explained Variance |
| plotdistanceratio | Histogram of Cell-to-Cell Distances in Real versus Embedded... |
| plotexpmap | Highlighting gene expression in a dimensional reduction... |
| plotExpNoise | Noise-expression scatter plot |
| plotfeatmap | Highlighting feature values in a dimensional reduction... |
| plotgraph | StemID2 Lineage Graph |
| plotjaccard | Plot Jaccard Similarities |
| plotlabelsmap | Plot labels in a dimensional reduction representation |
| plotlinkpv | Heatmap of Link P-values |
| plotlinkscore | Heatmap of Link Scores |
| plotmap | Plotting a dimensional reduction representation |
| plotmarkergenes | Plotting a Heatmap of Marker Gene Expression |
| plotMV | Plot of Mean-Variance dependence and various fits |
| plotNoiseModel | Function for plotting the baseline model of gene expression... |
| plotoutlierprobs | Plot Outlier Probabilities |
| plotPC | Function to plot the selected number of principal components |
| plotPearsonRes | Function for plotting the variance of Pearson residuals |
| plotPP | Plotting function for posterior checks |
| plotPT | Plotting pseudo-time in dimensional reduction representation |
| plotQQ | Scatter plot of two noise-related quantaties of local pruned... |
| plotQuantMap | Plotting noise-related quantaties of local pruned k-nearest... |
| plotRegNB | Function for plotting negative binomial regression |
| plotsaturation | Plot Saturation of Within-Cluster Dispersion |
| plotsensitivity | Plot Sensitivity |
| plotsilhouette | Plot Cluster Silhouette |
| plotspantree | Minimum Spanning Tree of RaceID3 clusters |
| plotsymbolsmap | Plotting groups as different symbols in a dimensional... |
| plotTrProbs | Function for plotting transition probabilities between... |
| plotUMINoise | Plotting noise dependence on total UMI count |
| postfntb | Posterior probability |
| priorfn | Prior function for maximum a posterior inference |
| projback | Compute Cell Projections for Randomized Background... |
| projcells | Compute transcriptome entropy of each cell |
| projenrichment | Enrichment of cells on inter-cluster links |
| pruneKnn | Function inferring a pruned knn matrix |
| pseudoTime | Extract pseudo-time order of cells along a trajectory |
| quantKnn | Noise-related quantaties of local pruned k-nearest... |
| RaceID-package | Identification of Cell Types, Inference of Lineage Trees, and... |
| rcpp_hello_world | Simple function using Rcpp |
| rfcorrect | Random Forests-based Reclassification |
| SCseq | The SCseq Class |
| Seurat2SCseq | Converting a Seurat object to a RaceID/VarID object |
| testPrior | Posterior check of the model |
| transitionProbs | Function for the computation of transition probabilities... |
| updateSC | Function for updating a RaceID SCseq object with VarID... |
| varRegression | Linear Regression of Sources of Variability |
| violinMarkerPlot | Violin plot of marker gene expression or noise |
