ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data


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Documentation for package ‘ILoReg’ version 1.16.0

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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