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

## Documentation for package ‘RaceID’ version 0.1.9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
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
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 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
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 the t-SNE map
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