Computation of a two dimensional t-SNE representation
Function for computing local gene expression averages
Function to create a knn matrix
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.
Computing a distance matrix for cell type inference
Compute transcriptome entropy of each cell
Computes Medoids from a Clustering Partition
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.
Computation of a two dimensional Fruchterman-Rheingold representation
Fitting a Gamma distribution to global cell-to-cell variability
Function for extracting genes with elevated variability in a cluster
Computation of a two dimensional umap representation
Function for extracting genes with differential biological variability in a cluster
Computing P-values for Link Significance
Dotplot of gene expression across clusters or samples
Compute StemID2 score
Function for extracting a filtered expression matrix from a RaceID SCseq object
Data filtering
Extracting filtered expression data
Function for filtering count data
Extract Projections of all Cells from a Cluster
Function for computing a background model of gene expression variability
Function for plottinhg the background model of gene expression variability
Function for plotting differentially variable genes
Inference of a Lineage Graph
Inference of outlier cells and final clustering
Function for filtering count data
Extract all genes for a module in a FateID self-orgaizing map
Compute Expression Differences between Clusters
Imputed expression matrix
Single-cell transcriptome data of intestinal epithelial cells
Function for infering clustering of the pruned k nearest neighbour graph
Function for differential expression analysis
Histogram of Cell-to-Cell Distances in Real versus Embedded Space
Plotting pseudo-time in dimensional reduction representation
Function for plotting the variance of Pearson residuals
Plotting function for posterior checks
Scatter plot of two noise-related quantaties of local pruned k-nearest neighbourhoods
Function for fitting a negative binomial noise model of technical and biological variability
Barplot of differentially expressed genes
Plot Jaccard Similarities
Plot Background Model
Plot Saturation of Within-Cluster Dispersion
Function for inspecting pruned k-nearest neighbourhoods
Plot Outlier Probabilities
Plotting noise-related quantaties of local pruned k-nearest neighbourhoods
Function for plotting differentially expressed genes
Highlighting gene expression in a dimensional reduction representation
Plotting the Saturation of Explained Variance
Single-cell transcriptome data of intestinal epithelial cells
Function for extracting genes maximal variability
Function for plotting negative binomial regression
Plot Sensitivity
Plot of Mean-Variance dependence and various fits
Noise-expression scatter plot
Function for extracting genes maximal variability
Plotting a dimensional reduction representation
Plot Cluster Silhouette
Function for fitting a negative binomial noise model of technical and biological variability
Plot labels in a dimensional reduction representation
Extract pseudo-time order of cells along a trajectory
Noise-related quantaties of local pruned k-nearest neighbourhoods
Function inferring a pruned knn matrix
Function for plotting transition probabilities between clusters
Plotting noise dependence on total UMI count
Plotting a Heatmap of Marker Gene Expression
Posterior probability
Enrichment of cells on inter-cluster links
Simple function using Rcpp
Compute transcriptome entropy of each cell
Compute Cell Projections for Randomized Background Distribution
Function for computing a fit to the baseline of gene expression variability
Boxplots for features across clusters
Function to plot the selected number of principal components
Prior function for maximum a posterior inference
Function for updating a RaceID SCseq object with VarID results
StemID2 Lineage Graph
Heatmap of Link Scores
Function for plotting the baseline model of gene expression variability
Linear Regression of Sources of Variability
Highlighting feature values in a dimensional reduction representation
Random Forests-based Reclassification
Heatmap of Link P-values
Violin plot of marker gene expression or noise
Minimum Spanning Tree of RaceID3 clusters
Function for the computation of transition probabilities between clusters
Plotting groups as different symbols in a dimensional reduction representation
Posterior check of the model
The SCseq Class
The Ltree Class
Baseline gene expression variability
Converting a Seurat object to a RaceID/VarID object
Dimensional Reduction by PCA or ICA
Function for calculating total variance from VarID fit
Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data
Gene Expression Barplot
Differential Gene Expression between Links
Function for calculating an aggregated dispersion parameter
Extract Cells on Differentiation Trajectory
Clustering of single-cell transcriptome data
Function for computing local gene expression variability
Inference of differentially expressed genes in a cluster
Function for pruning k-nearest neighborhoods based on neighborhood overlap
Function for calculating the total variance fit
Plotting a Heatmap of the Distance Matrix
Cell cycle markers for Mus Muscuus
Function for fitting a negative binomial noise model of technical and biological variability across cells in pruned k-nearest neighbourhoods.