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


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Documentation for package ‘RaceID’ version 0.2.3

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RaceID-package A short title line describing what the package does
barplotgene Gene Expression Barplot
baseLineVar Baseline gene expression variability
branchcells Differential Gene Expression between Links
CCcorrect Dimensional Reduction by PCA or ICA
cc_genes Cell cycle markers for Mus Muscuus
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
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
comptsne Computation of a two dimensional t-SNE representation
compumap Computation of a two dimensional umap representation
createKnnMatrix Function to create a knn matrix
diffexpnb Function for differential expression analysis
diffgenes Compute Expression Differences between Clusters
diffNoisyGenes Function for extracting genes with elevated variability in a cluster
filterdata Data filtering
findoutliers Inference of outlier cells and final clustering
fitBackVar Function for computing a background model of gene expression variability
fractDotPlot Dotplot of gene expression across clusters or samples
getExpData Function for extracting a filtered expression matrix from a 'RaceID' 'SCseq' object
getfdata Extracting filtered expression data
getproj Extract Projections of all Cells from a Cluster
graphCluster Function for infering Louvain clustering of the pruned k nearest neighbour graph
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
maxNoisyGenes Function for extracting genes maximal variability
noiseBaseFit Function for computing a fit to the baseline of gene expression variability
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
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
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
plotNoiseModel Function for plotting the baseline model of gene expression variability
plotoutlierprobs Plot Outlier Probabilities
plotPearsonRes Function for plotting the variance of Pearson residuals
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
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
RaceID A short title line describing what the package does
rcpp_hello_world Simple function using Rcpp
rfcorrect Random Forests-based Reclassification
SCseq The SCseq Class
SCseq-class The SCseq Class
transitionProbs Function for the computation of transition probabilities between clusters
updateSC Function for updating a RaceID SCseq object with VarID results
varRegression Linear Regression of Sources of Variability