RaceID0.3.9 package

Gene Expression Barplot

Baseline gene expression variability

Differential Gene Expression between Links

Function for calculating an aggregated dispersion parameter

Function for calculating total variance from VarID fit

Function for calculating the total variance fit

Dimensional Reduction by PCA or ICA

Extract Cells on Differentiation Trajectory

Function for pruning k-nearest neighborhoods based on neighborhood ove...

Inference of differentially expressed genes in a cluster

Clustering of single-cell transcriptome data

Plotting a Heatmap of the Distance Matrix

Computing a distance matrix for cell type inference

Compute transcriptome entropy of each cell

Computation of a two dimensional Fruchterman-Rheingold representation

Function for computing local gene expression averages

Computes Medoids from a Clustering Partition

Function for computing local gene expression variability

Computing P-values for Link Significance

Compute StemID2 score

Function for fitting a negative binomial noise model of technical and ...

Computation of a two dimensional t-SNE representation

Computation of a two dimensional umap representation

Function for regressing out the mean-variance dependence. This functio...

Function to create a knn matrix

Function for differential expression analysis

Compute Expression Differences between Clusters

Function for extracting genes with elevated variability in a cluster

Function for extracting genes with differential biological variability...

Function for filtering count data

Data filtering

Inference of outlier cells and final clustering

Function for computing a background model of gene expression variabili...

Fitting a Gamma distribution to global cell-to-cell variability

Second order polynomial fit of mean-variance dependence This function ...

Function for fitting a negative binomial noise model of technical and ...

Function for fitting a negative binomial noise model of technical and ...

Dotplot of gene expression across clusters or samples

Function for extracting a filtered expression matrix from a RaceID `...

Extracting filtered expression data

Function for filtering count data

Extract all genes for a module in a FateID self-orgaizing map

Extract Projections of all Cells from a Cluster

Function for infering clustering of the pruned k nearest neighbour gra...

Imputed expression matrix

Function for inspecting pruned k-nearest neighbourhoods

Inference of a Lineage Graph

The Ltree Class

Function for extracting genes maximal variability

Function for extracting genes maximal variability

Function for computing a fit to the baseline of gene expression variab...

Boxplots for features across clusters

Plot Background Model

Function for plottinhg the background model of gene expression variabi...

Barplot of differentially expressed genes

Function for plotting differentially expressed genes

Function for plotting differentially variable genes

Plotting the Saturation of Explained Variance

Histogram of Cell-to-Cell Distances in Real versus Embedded Space

Highlighting gene expression in a dimensional reduction representation

Noise-expression scatter plot

Highlighting feature values in a dimensional reduction representation

StemID2 Lineage Graph

Plot Jaccard Similarities

Plot labels in a dimensional reduction representation

Heatmap of Link P-values

Heatmap of Link Scores

Plotting a dimensional reduction representation

Plotting a Heatmap of Marker Gene Expression

Plot of Mean-Variance dependence and various fits

Function for plotting the baseline model of gene expression variabilit...

Plot Outlier Probabilities

Function to plot the selected number of principal components

Function for plotting the variance of Pearson residuals

Plotting function for posterior checks

Plotting pseudo-time in dimensional reduction representation

Scatter plot of two noise-related quantaties of local pruned k-nearest...

Plotting noise-related quantaties of local pruned k-nearest neighbourh...

Function for plotting negative binomial regression

Plot Saturation of Within-Cluster Dispersion

Plot Sensitivity

Plot Cluster Silhouette

Minimum Spanning Tree of RaceID3 clusters

Plotting groups as different symbols in a dimensional reduction repres...

Function for plotting transition probabilities between clusters

Plotting noise dependence on total UMI count

Posterior probability

Prior function for maximum a posterior inference

Compute Cell Projections for Randomized Background Distribution

Compute transcriptome entropy of each cell

Enrichment of cells on inter-cluster links

Function inferring a pruned knn matrix

Extract pseudo-time order of cells along a trajectory

Noise-related quantaties of local pruned k-nearest neighbourhoods

Identification of Cell Types, Inference of Lineage Trees, and Predicti...

Simple function using Rcpp

Random Forests-based Reclassification

The SCseq Class

Converting a Seurat object to a RaceID/VarID object

Posterior check of the model

Function for the computation of transition probabilities between clust...

Function for updating a RaceID SCseq object with VarID results

Linear Regression of Sources of Variability

Violin plot of marker gene expression or noise