| 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 |
| CCcorrect |
Dimensional Reduction by PCA or ICA |
| 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 |
| 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 |
| compTBNoise |
Function for fitting a negative binomial noise model of technical and biological variability across cells in pruned k-nearest neighbourhoods. |
| 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 |
| plotB |
Boxplots for features across clusters |
| 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 |
| plotDiffNoise |
Function for plotting differentially variable 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 |
| plotExpNoise |
Noise-expression scatter plot |
| 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 |
| plotMV |
Plot of Mean-Variance dependence and various fits |
| plotNoiseModel |
Function for plotting the baseline model of gene expression variability |
| plotoutlierprobs |
Plot Outlier Probabilities |
| plotPC |
Function to plot the selected number of principal components |
| plotPearsonRes |
Function for plotting the variance of Pearson residuals |
| plotPP |
Plotting function for posterior checks |
| plotPT |
Plotting pseudo-time in dimensional reduction representation |
| 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 |
| 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 |
| plotUMINoise |
Plotting noise dependence on total UMI count |
| 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 |