barplotgene | Gene Expression Barplot |
branchcells | Differential Gene Expression between Links |
CCcorrect | Dimensional Reduction by PCA or ICA |
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 |
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 |
diffexpnb | Function for differential expression analysis |
diffgenes | Compute Expression Differences between Clusters |
filterdata | Data filtering |
findoutliers | Inference of outlier cells and final clustering |
getfdata | Extracting filtered expression data |
getproj | Extract Projections of all Cells from a Cluster |
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 |
Ltree | The Ltree Class |
Ltree-class | The Ltree Class |
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 |
plotprojections | Two-Dimensional Map of Cell Projections |
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 |
rfcorrect | Random Forests-based Reclassification |
SCseq | The SCseq Class |
SCseq-class | The SCseq Class |
varRegression | Linear Regression of Sources of Variability |