Identification of Cell Types and Inference of Lineage Trees from Single-Cell RNA-Seq Data

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Documentation for package ‘RaceID’ version 0.1.1

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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