AnnotationScatterPlot | Visualiation of a custom annotation over nonlinear dimensionality reduction |
AnnotationScatterPlot-method | Visualiation of a custom annotation over nonlinear dimensionality reduction |
AnnotationScatterPlot.SingleCellExperiment | Visualiation of a custom annotation over nonlinear dimensionality reduction |
CalcSilhInfo | Estimating optimal K using silhouette |
CalcSilhInfo-method | Estimating optimal K using silhouette |
CalcSilhInfo.SingleCellExperiment | Estimating optimal K using silhouette |
ClusteringScatterPlot | Visualize the clustering over nonliner dimensionality reduction |
ClusteringScatterPlot-method | Visualize the clustering over nonliner dimensionality reduction |
ClusteringScatterPlot.SingleCellExperiment | Visualize the clustering over nonliner dimensionality reduction |
DownOverSampling | Down- and oversample data |
FindAllGeneMarkers | identification of gene markers for all clusters |
FindAllGeneMarkers-method | identification of gene markers for all clusters |
FindAllGeneMarkers.SingleCellExperiment | identification of gene markers for all clusters |
FindGeneMarkers | Identification of gene markers for a cluster or two arbitrary combinations of clusters |
FindGeneMarkers-method | Identification of gene markers for a cluster or two arbitrary combinations of clusters |
FindGeneMarkers.SingleCellExperiment | Identification of gene markers for a cluster or two arbitrary combinations of clusters |
GeneHeatmap | Heatmap visualization of the gene markers identified by FindAllGeneMarkers |
GeneHeatmap-method | Heatmap visualization of the gene markers identified by FindAllGeneMarkers |
GeneHeatmap.SingleCellExperiment | Heatmap visualization of the gene markers identified by FindAllGeneMarkers |
GeneScatterPlot | Visualize gene expression over nonlinear dimensionality reduction |
GeneScatterPlot-method | Visualize gene expression over nonlinear dimensionality reduction |
GeneScatterPlot.SingleCellExperiment | Visualize gene expression over nonlinear dimensionality reduction |
HierarchicalClustering | Hierarchical clustering using the Ward's method |
HierarchicalClustering-method | Hierarchical clustering using the Ward's method |
HierarchicalClustering.SingleCellExperiment | Hierarchical clustering using the Ward's method |
LogisticRegression | Clustering projection using logistic regression from the LiblineaR R package |
MergeClusters | Merge clusters |
MergeClusters-method | Merge clusters |
MergeClusters.SingleCellExperiment | Merge clusters |
pbmc3k_500 | A toy dataset with 500 cells downsampled from the pbmc3k dataset. |
PCAElbowPlot | Elbow plot of the standard deviations of the principal components |
PCAElbowPlot-method | Elbow plot of the standard deviations of the principal components |
PCAElbowPlot.SingleCellExperiment | Elbow plot of the standard deviations of the principal components |
PrepareILoReg | Prepare 'SingleCellExperiment' object for 'ILoReg' analysis |
PrepareILoReg-method | Prepare 'SingleCellExperiment' object for 'ILoReg' analysis |
PrepareILoReg.SingleCellExperiment | Prepare 'SingleCellExperiment' object for 'ILoReg' analysis |
RenameAllClusters | Renaming all clusters at once |
RenameAllClusters-method | Renaming all clusters at once |
RenameAllClusters.SingleCellExperiment | Renaming all clusters at once |
RenameCluster | Renaming one cluster |
RenameCluster-method | Renaming one cluster |
RenameCluster.SingleCellExperiment | Renaming one cluster |
RunICP | Iterative Clustering Projection (ICP) clustering |
RunParallelICP | Run ICP runs parallerly |
RunParallelICP-method | Run ICP runs parallerly |
RunParallelICP.SingleCellExperiment | Run ICP runs parallerly |
RunPCA | PCA transformation of the joint probability matrix |
RunPCA-method | PCA transformation of the joint probability matrix |
RunPCA.SingleCellExperiment | PCA transformation of the joint probability matrix |
RunTSNE | Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding (t-SNE) |
RunTSNE-method | Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding (t-SNE) |
RunTSNE.SingleCellExperiment | Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding (t-SNE) |
RunUMAP | Uniform Manifold Approximation and Projection (UMAP) |
RunUMAP-method | Uniform Manifold Approximation and Projection (UMAP) |
RunUMAP.SingleCellExperiment | Uniform Manifold Approximation and Projection (UMAP) |
SelectKClusters | Selecting K clusters from hierarchical clustering |
SelectKClusters-method | Selecting K clusters from hierarchical clustering |
SelectKClusters.SingleCellExperiment | Selecting K clusters from hierarchical clustering |
SelectTopGenes | Select top or bottom N genes based on a selection criterion |
SilhouetteCurve | Silhouette curve |
SilhouetteCurve-method | Silhouette curve |
SilhouetteCurve.SingleCellExperiment | Silhouette curve |
VlnPlot | Gene expression visualization using violin plots |
VlnPlot-method | Gene expression visualization using violin plots |
VlnPlot.SingleCellExperiment | Gene expression visualization using violin plots |