CCcorrect               Dimensional Reduction by PCA or ICA
Ltree-class             The Ltree Class
RaceID-package          A short title line describing what the package
                        does
SCseq                   The SCseq Class
barplotgene             Gene Expression Barplot
baseLineVar             Baseline gene expression variability
branchcells             Differential Gene Expression between Links
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
compNoise               Function for computing local gene expression
                        variability
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
compmedoids             Computes Medoids from a Clustering Partition
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
diffNoisyGenes          Function for extracting genes with elevated
                        variability in a cluster
diffexpnb               Function for differential expression analysis
diffgenes               Compute Expression Differences between Clusters
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
maxNoisyGenes           Function for extracting genes maximal
                        variability
noiseBaseFit            Function for computing a fit to the baseline of
                        gene expression variability
plotBackVar             Function for plottinhg the background model of
                        gene expression variability
plotNoiseModel          Function for plotting the baseline model of
                        gene expression variability
plotPearsonRes          Function for plotting the variance of Pearson
                        residuals
plotRegNB               Function for plotting negative binomial
                        regression
plotTrProbs             Function for plotting transition probabilities
                        between clusters
plotbackground          Plot Background Model
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 the t-SNE map
plotgraph               StemID2 Lineage Graph
plotjaccard             Plot Jaccard Similarities
plotlabelsmap           Plot labels in the t-SNE map
plotlinkpv              Heatmap of Link P-values
plotlinkscore           Heatmap of Link Scores
plotmap                 Plotting a t-SNE map
plotmarkergenes         Plotting a Heatmap of Marker Gene Expression
plotoutlierprobs        Plot Outlier Probabilities
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 the
                        t-SNE map
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
rcpp_hello_world        Simple function using Rcpp
rfcorrect               Random Forests-based Reclassification
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
