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RaceID (version 0.1.3)
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, Gr
n D. (2018)
.
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Install
install.packages('RaceID')
Monthly Downloads
505
Version
0.1.3
License
GPL-3
Maintainer
Dominic Grc3<bc>n
Last Published
January 22nd, 2019
Functions in RaceID (0.1.3)
Search functions
clustheatmap
Plotting a Heatmap of the Distance Matrix
compscore
Compute StemID2 score
comptsne
Computation of a two dimensional t-SNE representation
compdist
Computing a distance matrix for cell type inference
imputeexp
Imputed expression matrix
compfr
Computation of a two dimensional Fruchterman-Rheingold representation
compentropy
Compute transcriptome entropy of each cell
plotdistanceratio
Histogram of Cell-to-Cell Distances in Real versus Embedded Space
clustexp
Clustering of single-cell transcriptome data
intestinalData
Single-cell transcriptome data of intestinal epithelial cells
plotdiffgenesnb
Function for plotting differentially expressed genes
findoutliers
Inference of outlier cells and final clustering
plotmap
Plotting a t-SNE map
lineagegraph
Inference of a Lineage Graph
plotdimsat
Plotting the Saturation of Explained Variance
plotlinkscore
Heatmap of Link Scores
plotspantree
Minimum Spanning Tree of RaceID3 clusters
plotgraph
StemID2 Lineage Graph
plotjaccard
Plot Jaccard Similarities
intestinalDataSmall
Single-cell transcriptome data of intestinal epithelial cells
plotexpmap
Highlighting gene expression in the t-SNE map
compmedoids
Computes Medoids from a Clustering Partition
diffexpnb
Function for differential expression analysis
Ltree-class
The Ltree Class
plotsensitivity
Plot Sensitivity
diffgenes
Compute Expression Differences between Clusters
plotsilhouette
Plot Cluster Silhouette
plotdiffgenes
Barplot of differentially expressed genes
plotbackground
Plot Background Model
comppvalue
Computing P-values for Link Significance
projback
Compute Cell Projections for Randomized Background Distribution
plotlabelsmap
Plot labels in the t-SNE map
plotsymbolsmap
Plotting groups as different symbols in the t-SNE map
plotlinkpv
Heatmap of Link P-values
getfdata
Extracting filtered expression data
projcells
Compute transcriptome entropy of each cell
projenrichment
Enrichment of cells on inter-cluster links
rfcorrect
Random Forests-based Reclassification
getproj
Extract Projections of all Cells from a Cluster
varRegression
Linear Regression of Sources of Variability
plotmarkergenes
Plotting a Heatmap of Marker Gene Expression
plotoutlierprobs
Plot Outlier Probabilities
plotprojections
Two-Dimensional Map of Cell Projections
plotsaturation
Plot Saturation of Within-Cluster Dispersion
CCcorrect
Dimensional Reduction by PCA or ICA
SCseq
The SCseq Class
barplotgene
Gene Expression Barplot
filterdata
Data filtering
branchcells
Differential Gene Expression between Links
clustdiffgenes
Inference of differentially expressed genes in a cluster
cellsfromtree
Extract Cells on Differentiation Trajectory