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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, Grn D. (2018) .

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Version

Install

install.packages('RaceID')

Monthly Downloads

358

Version

0.1.3

License

GPL-3

Maintainer

Dominic Grc3<bc>n

Last Published

January 22nd, 2019

Functions in RaceID (0.1.3)

Plotting a Heatmap of the Distance Matrix

Compute StemID2 score

Computation of a two dimensional t-SNE representation

Computing a distance matrix for cell type inference

Imputed expression matrix

Computation of a two dimensional Fruchterman-Rheingold representation

Compute transcriptome entropy of each cell

plotdistanceratio

Histogram of Cell-to-Cell Distances in Real versus Embedded Space

Clustering of single-cell transcriptome data

Single-cell transcriptome data of intestinal epithelial cells

plotdiffgenesnb

Function for plotting differentially expressed genes

Inference of outlier cells and final clustering

Plotting a t-SNE map

Inference of a Lineage Graph

Plotting the Saturation of Explained Variance

Heatmap of Link Scores

Minimum Spanning Tree of RaceID3 clusters

StemID2 Lineage Graph

Plot Jaccard Similarities

intestinalDataSmall

Single-cell transcriptome data of intestinal epithelial cells

Highlighting gene expression in the t-SNE map

Computes Medoids from a Clustering Partition

Function for differential expression analysis

The Ltree Class

plotsensitivity

Plot Sensitivity

Compute Expression Differences between Clusters

Plot Cluster Silhouette

Barplot of differentially expressed genes

Plot Background Model

Computing P-values for Link Significance

Compute Cell Projections for Randomized Background Distribution

Plot labels in the t-SNE map

Plotting groups as different symbols in the t-SNE map

Heatmap of Link P-values

Extracting filtered expression data

Compute transcriptome entropy of each cell

Enrichment of cells on inter-cluster links

Random Forests-based Reclassification

Extract Projections of all Cells from a Cluster

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

Plot Saturation of Within-Cluster Dispersion

Dimensional Reduction by PCA or ICA

The SCseq Class

Gene Expression Barplot

Differential Gene Expression between Links

Inference of differentially expressed genes in a cluster

Extract Cells on Differentiation Trajectory