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 |
barplotgene | Gene Expression Barplot |
baseLineVar | Baseline gene expression variability |
branchcells | Differential Gene Expression between Links |
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 |
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 |
extractCounts | Function for filtering count data |
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 |
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 |
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 |
lineagegraph | Inference of a Lineage Graph |
Ltree | The Ltree Class |
Ltree-class | The Ltree Class |
maxNoisyGenes | Function for extracting genes maximal variability |
maxNoisyGenesTB | Function for extracting genes maximal variability |
noiseBaseFit | Function for computing a fit to the baseline of gene expression variability |
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 |
quantKnn | Noise-related quantaties of local pruned k-nearest neighbourhoods |
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 |
SCseq | The SCseq Class |
SCseq-class | The SCseq Class |
Seurat2SCseq | Converting a Seurat object to a RaceID/VarID object |
testPrior | Posterior check of the model |
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 |
violinMarkerPlot | Violin plot of marker gene expression or noise |