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

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Documentation for package ‘ILoReg’ version 1.19.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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