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

AnnotationScatterPlotVisualiation of a custom annotation over nonlinear...
CalcSilhInfoEstimating optimal K using silhouette
ClusteringScatterPlotVisualize the clustering over nonliner dimensionality...
DownOverSamplingDown- and oversample data
FindAllGeneMarkersidentification of gene markers for all clusters
FindGeneMarkersIdentification of gene markers for a cluster or two arbitrary...
GeneHeatmapHeatmap visualization of the gene markers identified by...
GeneScatterPlotVisualize gene expression over nonlinear dimensionality...
HierarchicalClusteringHierarchical clustering using the Ward's method
LogisticRegressionClustering projection using logistic regression from the...
MergeClustersMerge clusters
pbmc3k_500A toy dataset with 500 cells downsampled from the pbmc3k...
PCAElbowPlotElbow plot of the standard deviations of the principal...
PrepareILoRegPrepare 'SingleCellExperiment' object for 'ILoReg' analysis
RenameAllClustersRenaming all clusters at once
RenameClusterRenaming one cluster
RunICPIterative Clustering Projection (ICP) clustering
RunParallelICPRun ICP runs parallerly
RunPCAPCA transformation of the joint probability matrix
RunTSNEBarnes-Hut implementation of t-Distributed Stochastic...
RunUMAPUniform Manifold Approximation and Projection (UMAP)
SelectKClustersSelecting K clusters from hierarchical clustering
SelectTopGenesSelect top or bottom N genes based on a selection criterion
SilhouetteCurveSilhouette curve
VlnPlotGene expression visualization using violin plots
ILoReg documentation built on Nov. 8, 2020, 8:20 p.m.