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