| RaceID-package | A short title line describing what the package does |
| barplotgene | Gene Expression Barplot |
| baseLineVar | Baseline gene expression variability |
| branchcells | Differential Gene Expression between Links |
| CCcorrect | Dimensional Reduction by PCA or ICA |
| cc_genes | Cell cycle markers for Mus Muscuus |
| cellsfromtree | Extract Cells on Differentiation Trajectory |
| 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 representation |
| 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 |
| comptsne | Computation of a two dimensional t-SNE representation |
| compumap | Computation of a two dimensional umap representation |
| 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 cluster |
| filterdata | Data filtering |
| findoutliers | Inference of outlier cells and final clustering |
| fitBackVar | Function for computing a background model of gene expression variability |
| fractDotPlot | Dotplot of gene expression across clusters or samples |
| getExpData | Function for extracting a filtered expression matrix from a 'RaceID' 'SCseq' object |
| getfdata | Extracting filtered expression data |
| getproj | Extract Projections of all Cells from a Cluster |
| graphCluster | Function for infering Louvain clustering of the pruned k nearest neighbour graph |
| imputeexp | Imputed expression matrix |
| 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 |
| Ltree-class | The Ltree Class |
| maxNoisyGenes | Function for extracting genes maximal variability |
| noiseBaseFit | Function for computing a fit to the baseline of gene expression variability |
| plotbackground | Plot Background Model |
| plotBackVar | Function for plottinhg the background model of gene expression variability |
| plotdiffgenes | Barplot of differentially expressed genes |
| plotdiffgenesnb | Function for plotting differentially expressed genes |
| plotdimsat | Plotting the Saturation of Explained Variance |
| plotdistanceratio | Histogram of Cell-to-Cell Distances in Real versus Embedded Space |
| plotexpmap | Highlighting gene expression in a dimensional reduction representation |
| 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 |
| plotNoiseModel | Function for plotting the baseline model of gene expression variability |
| plotoutlierprobs | Plot Outlier Probabilities |
| plotPearsonRes | Function for plotting the variance of Pearson residuals |
| 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 reduction representation |
| plotTrProbs | Function for plotting transition probabilities between clusters |
| projback | Compute Cell Projections for Randomized Background Distribution |
| projcells | Compute transcriptome entropy of each cell |
| projenrichment | Enrichment of cells on inter-cluster links |
| pruneKnn | Function inferring a pruned knn matrix |
| RaceID | A short title line describing what the package does |
| rcpp_hello_world | Simple function using Rcpp |
| rfcorrect | Random Forests-based Reclassification |
| SCseq | The SCseq Class |
| SCseq-class | The SCseq Class |
| transitionProbs | Function for the computation of transition probabilities between clusters |
| updateSC | Function for updating a RaceID SCseq object with VarID results |
| varRegression | Linear Regression of Sources of Variability |