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

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Documentation for package ‘RaceID’ version 0.3.5

• 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