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RaceID (version 0.2.3)
Identification of Cell Types and Inference of Lineage Trees from Single-Cell RNA-Seq Data
Description
Application of 'RaceID' allows inference of cell types and prediction of lineage trees by he StemID2 algorithm. Herman, J.S., Sagar, Grün D. (2018)
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Install
install.packages('RaceID')
Monthly Downloads
505
Version
0.2.3
License
GPL-3
Maintainer
Dominic Grc3<bc>n
Last Published
April 8th, 2021
Functions in RaceID (0.2.3)
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Ltree-class
The Ltree Class
cellsfromtree
Extract Cells on Differentiation Trajectory
CCcorrect
Dimensional Reduction by PCA or ICA
cc_genes
Cell cycle markers for Mus Muscuus
baseLineVar
Baseline gene expression variability
barplotgene
Gene Expression Barplot
SCseq
The SCseq Class
branchcells
Differential Gene Expression between Links
clustdiffgenes
Inference of differentially expressed genes in a cluster
RaceID-package
A short title line describing what the package does
comppvalue
Computing P-values for Link Significance
findoutliers
Inference of outlier cells and final clustering
clustheatmap
Plotting a Heatmap of the Distance Matrix
noiseBaseFit
Function for computing a fit to the baseline of gene expression variability
clustexp
Clustering of single-cell transcriptome data
maxNoisyGenes
Function for extracting genes maximal variability
filterdata
Data filtering
compmedoids
Computes Medoids from a Clustering Partition
compfr
Computation of a two dimensional Fruchterman-Rheingold representation
compMean
Function for computing local gene expression averages
compNoise
Function for computing local gene expression variability
createKnnMatrix
Function to create a knn matrix
diffgenes
Compute Expression Differences between Clusters
diffexpnb
Function for differential expression analysis
fitBackVar
Function for computing a background model of gene expression variability
lineagegraph
Inference of a Lineage Graph
diffNoisyGenes
Function for extracting genes with elevated variability in a cluster
plotmap
Plotting a dimensional reduction representation
intestinalDataSmall
Single-cell transcriptome data of intestinal epithelial cells
compentropy
Compute transcriptome entropy of each cell
compdist
Computing a distance matrix for cell type inference
plotmarkergenes
Plotting a Heatmap of Marker Gene Expression
getproj
Extract Projections of all Cells from a Cluster
fractDotPlot
Dotplot of gene expression across clusters or samples
plotdiffgenes
Barplot of differentially expressed genes
plotdistanceratio
Histogram of Cell-to-Cell Distances in Real versus Embedded Space
comptsne
Computation of a two dimensional t-SNE representation
compscore
Compute StemID2 score
imputeexp
Imputed expression matrix
plotdimsat
Plotting the Saturation of Explained Variance
graphCluster
Function for infering Louvain clustering of the pruned k nearest neighbour graph
intestinalData
Single-cell transcriptome data of intestinal epithelial cells
compumap
Computation of a two dimensional umap representation
plotPearsonRes
Function for plotting the variance of Pearson residuals
getExpData
Function for extracting a filtered expression matrix from a
RaceID
SCseq
object
plotBackVar
Function for plottinhg the background model of gene expression variability
plotsensitivity
Plot Sensitivity
plotsilhouette
Plot Cluster Silhouette
plotdiffgenesnb
Function for plotting differentially expressed genes
plotlinkpv
Heatmap of Link P-values
plotRegNB
Function for plotting negative binomial regression
rcpp_hello_world
Simple function using Rcpp
transitionProbs
Function for the computation of transition probabilities between clusters
rfcorrect
Random Forests-based Reclassification
plotlinkscore
Heatmap of Link Scores
getfdata
Extracting filtered expression data
updateSC
Function for updating a RaceID SCseq object with VarID results
plotexpmap
Highlighting gene expression in a dimensional reduction representation
plotNoiseModel
Function for plotting the baseline model of gene expression variability
plotgraph
StemID2 Lineage Graph
plotbackground
Plot Background Model
plotjaccard
Plot Jaccard Similarities
plotTrProbs
Function for plotting transition probabilities between clusters
plotsaturation
Plot Saturation of Within-Cluster Dispersion
plotspantree
Minimum Spanning Tree of RaceID3 clusters
plotoutlierprobs
Plot Outlier Probabilities
projenrichment
Enrichment of cells on inter-cluster links
plotlabelsmap
Plot labels in a dimensional reduction representation
pruneKnn
Function inferring a pruned knn matrix
plotsymbolsmap
Plotting groups as different symbols in a dimensional reduction representation
projback
Compute Cell Projections for Randomized Background Distribution
varRegression
Linear Regression of Sources of Variability
projcells
Compute transcriptome entropy of each cell