CCcorrect               Dimensional Reduction by PCA or ICA
Ltree-class             The Ltree Class
RaceID-package          Identification of Cell Types, Inference of
                        Lineage Trees, and Prediction of Noise Dynamics
                        from Single-Cell RNA-Seq Data
SCseq                   The SCseq Class
Seurat2SCseq            Converting a Seurat object to a RaceID/VarID
                        object
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
cc_genes                Cell cycle markers for Mus Muscuus
cellsfromtree           Extract Cells on Differentiation Trajectory
cleanNN                 Function for pruning k-nearest neighborhoods
                        based on neighborhood overlap
clustdiffgenes          Inference of differentially expressed genes in
                        a cluster
clustexp                Clustering of single-cell transcriptome data
clustheatmap            Plotting a Heatmap of the Distance Matrix
compMean                Function for computing local gene expression
                        averages
compNoise               Function for computing local gene expression
                        variability
compTBNoise             Function for fitting a negative binomial noise
                        model of technical and biological variability
                        across cells in pruned k-nearest
                        neighbourhoods.
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
corrVar                 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.
createKnnMatrix         Function to create a knn matrix
diffNoisyGenes          Function for extracting genes with elevated
                        variability in a cluster
diffNoisyGenesTB        Function for extracting genes with differential
                        biological variability in a cluster
diffexpnb               Function for differential expression analysis
diffgenes               Compute Expression Differences between Clusters
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 variability
fitGammaRt              Fitting a Gamma distribution to global
                        cell-to-cell variability
fitLogVarLogMean        Second order polynomial fit of mean-variance
                        dependence This function corrects for the
                        systematic dependence of the variance on the
                        mean by a local regression.
fitNBtb                 Function for fitting a negative binomial noise
                        model of technical and biological variability
fitNBtbCl               Function for fitting a negative binomial noise
                        model of technical and biological variability
fractDotPlot            Dotplot of gene expression across clusters or
                        samples
getExpData              Function for extracting a filtered expression
                        matrix from a 'RaceID' 'SCseq' object
getFilteredCounts       Function for filtering count data
getNode                 Extract all genes for a module in a FateID
                        self-orgaizing map
getfdata                Extracting filtered expression data
getproj                 Extract Projections of all Cells from a Cluster
graphCluster            Function for infering clustering of the pruned
                        k nearest neighbour graph
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
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 expression variability
plotB                   Boxplots for features across clusters
plotBackVar             Function for plottinhg the background model of
                        gene expression variability
plotDiffNoise           Function for plotting differentially variable
                        genes
plotExpNoise            Noise-expression scatter plot
plotMV                  Plot of Mean-Variance dependence and various
                        fits
plotNoiseModel          Function for plotting the baseline model of
                        gene expression variability
plotPC                  Function to plot the selected number of
                        principal components
plotPP                  Plotting function for posterior checks
plotPT                  Plotting pseudo-time in dimensional reduction
                        representation
plotPearsonRes          Function for plotting the variance of Pearson
                        residuals
plotQQ                  Scatter plot of two noise-related quantaties of
                        local pruned k-nearest neighbourhoods
plotQuantMap            Plotting noise-related quantaties of local
                        pruned k-nearest neighbourhoods
plotRegNB               Function for plotting negative binomial
                        regression
plotTrProbs             Function for plotting transition probabilities
                        between clusters
plotUMINoise            Plotting noise dependence on total UMI count
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 a dimensional
                        reduction representation
plotfeatmap             Highlighting feature values 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
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 a
                        dimensional reduction representation
postfntb                Posterior probability
priorfn                 Prior function for maximum a posterior
                        inference
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
pseudoTime              Extract pseudo-time order of cells along a
                        trajectory
quantKnn                Noise-related quantaties of local pruned
                        k-nearest neighbourhoods
rcpp_hello_world        Simple function using Rcpp
rfcorrect               Random Forests-based Reclassification
testPrior               Posterior check of the model
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
violinMarkerPlot        Violin plot of marker gene expression or noise
