RaceID-package |
A short title line describing what the package does |
barplotgene |
Gene Expression Barplot |
baseLineVar |
Baseline gene expression variability |
branchcells |
Differential Gene Expression between Links |
CCcorrect |
Dimensional Reduction by PCA or ICA |
cc_genes |
Cell cycle markers for Mus Muscuus |
cellsfromtree |
Extract Cells on Differentiation Trajectory |
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 |
comptsne |
Computation of a two dimensional t-SNE representation |
compumap |
Computation of a two dimensional umap representation |
createKnnMatrix |
Function to create a knn matrix |
diffexpnb |
Function for differential expression analysis |
diffgenes |
Compute Expression Differences between Clusters |
diffNoisyGenes |
Function for extracting genes with elevated variability in a cluster |
filterdata |
Data filtering |
findoutliers |
Inference of outlier cells and final clustering |
fitBackVar |
Function for computing a background model of gene expression variability |
fractDotPlot |
Dotplot of gene expression across clusters or samples |
getExpData |
Function for extracting a filtered expression matrix from a 'RaceID' 'SCseq' object |
getfdata |
Extracting filtered expression data |
getproj |
Extract Projections of all Cells from a Cluster |
graphCluster |
Function for infering Louvain clustering of the pruned k nearest neighbour graph |
imputeexp |
Imputed expression matrix |
intestinalData |
Single-cell transcriptome data of intestinal epithelial cells |
intestinalDataSmall |
Single-cell transcriptome data of intestinal epithelial cells |
lineagegraph |
Inference of a Lineage Graph |
Ltree |
The Ltree Class |
Ltree-class |
The Ltree Class |
maxNoisyGenes |
Function for extracting genes maximal variability |
noiseBaseFit |
Function for computing a fit to the baseline of gene expression variability |
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 |
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 |
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 |
plotNoiseModel |
Function for plotting the baseline model of gene expression variability |
plotoutlierprobs |
Plot Outlier Probabilities |
plotPearsonRes |
Function for plotting the variance of Pearson residuals |
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 |
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 |
RaceID |
A short title line describing what the package does |
rcpp_hello_world |
Simple function using Rcpp |
rfcorrect |
Random Forests-based Reclassification |
SCseq |
The SCseq Class |
SCseq-class |
The SCseq Class |
transitionProbs |
Function for the computation of transition probabilities between clusters |
updateSC |
Function for updating a RaceID SCseq object with VarID results |
varRegression |
Linear Regression of Sources of Variability |