# Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

## Documentation for package ‘RaceID’ version 0.4.0

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

## Help Pages

B C D E F G I L M N P Q R S T U V

RaceID-package | Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

## -- B --

barplotgene | Gene Expression Barplot
baseLineVar | Baseline gene expression variability
branchcells | Differential Gene Expression between Links

## -- C --

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

## -- D --

diffexpnb | Function for differential expression analysis
diffgenes | Compute Expression Differences between Clusters
diffNoisyGenes | Function for extracting genes with elevated variability in a cluster
diffNoisyGenesTB | Function for extracting genes with differential biological variability in a cluster

## -- E --

extractCounts | Function for filtering count data

## -- F --

filterdata | Data filtering
findoutliers | Inference of outlier cells and final clustering
fitBackVar | Function for computing a background model of gene expression variability
fitGammaRt | Fitting a Gamma distribution to global cell-to-cell variability
fitLogVarLogMean | Second order polynomial fit of mean-variance dependence This function corrects for the systematic dependence of the variance on the mean by a local regression.
fitNBtb | Function for fitting a negative binomial noise model of technical and biological variability
fitNBtbCl | Function for fitting a negative binomial noise model of technical and biological variability
fractDotPlot | Dotplot of gene expression across clusters or samples

## -- G --

getExpData | Function for extracting a filtered expression matrix from a 'RaceID' 'SCseq' object
getfdata | Extracting filtered expression data
getFilteredCounts | Function for filtering count data
getNode | Extract all genes for a module in a FateID self-orgaizing map
getproj | Extract Projections of all Cells from a Cluster
graphCluster | Function for infering clustering of the pruned k nearest neighbour graph

## -- I --

imputeexp | Imputed expression matrix
inspectKNN | Function for inspecting pruned k-nearest neighbourhoods
intestinalData | Single-cell transcriptome data of intestinal epithelial cells
intestinalDataSmall | Single-cell transcriptome data of intestinal epithelial cells

## -- L --

lineagegraph | Inference of a Lineage Graph
Ltree | The Ltree Class
Ltree-class | The Ltree Class

## -- M --

maxNoisyGenes | Function for extracting genes maximal variability
maxNoisyGenesTB | Function for extracting genes maximal variability

## -- N --

noiseBaseFit | Function for computing a fit to the baseline of gene expression variability

## -- P --

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

## -- Q --

quantKnn | Noise-related quantaties of local pruned k-nearest neighbourhoods

## -- R --

RaceID | Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data
rcpp_hello_world | Simple function using Rcpp
rfcorrect | Random Forests-based Reclassification

## -- S --

SCseq | The SCseq Class
SCseq-class | The SCseq Class
Seurat2SCseq | Converting a Seurat object to a RaceID/VarID object

## -- T --

testPrior | Posterior check of the model
transitionProbs | Function for the computation of transition probabilities between clusters

## -- U --

updateSC | Function for updating a RaceID SCseq object with VarID results

## -- V --

varRegression | Linear Regression of Sources of Variability
violinMarkerPlot | Violin plot of marker gene expression or noise