Man pages for SuperCell
Simplification of scRNA-Seq Data by Merging Together Similar Cells
| anndata_2_supercell | Convert Anndata metacell object (Metacell-2 or SEACells) to... |
| build_knn_graph | Build kNN graph |
| build_knn_graph_nn2 | Build kNN graph using RANN::nn2 (used in '"build_knn_graph"') |
| cell_lines | Cancer cell lines dataset |
| knn_graph_from_dist | Build kNN graph from distance (used in '"build_knn_graph"') |
| metacell2_anndata_2_supercell | Convert Metacells (Metacell-2) to Super-cell like object |
| SCimplify | Detection of metacells with the SuperCell approach |
| SCimplify_for_velocity | Construct super-cells from spliced and un-spliced matrices |
| SCimplify_from_embedding | Detection of metacells with the SuperCell approach from low... |
| sc_mixing_score | Compute mixing of single-cells within supercell |
| supercell_2_sce | Super-cells to SingleCellExperiment object |
| supercell_2_Seurat | Super-cells to Seurat object |
| supercell_assign | Assign super-cells to the most aboundant cluster |
| supercell_cluster | Cluster super-cell data |
| supercell_DimPlot | Plot metacell 2D plot (PCA, UMAP, tSNE etc) |
| supercell_estimate_velocity | Run RNAvelocity for super-cells (slightly modified from... |
| supercell_FindAllMarkers | Differential expression analysis of supep-cell data. Most of... |
| supercell_FindMarkers | Differential expression analysis of supep-cell data. Most of... |
| supercell_GE | Simplification of scRNA-seq dataset |
| supercell_GE_idx | Simplification of scRNA-seq dataset (old version, not used... |
| supercell_GeneGenePlot | Gene-gene correlation plot |
| supercell_GeneGenePlot_single | Plot Gene-gene correlation plot for 1 feature |
| supercell_merge | Merging independent SuperCell objects |
| supercell_mergeGE | Merging metacell gene expression matrices from several... |
| supercell_plot | Plot metacell NW |
| supercell_plot_GE | Plot super-cell NW colored by an expression of a gene... |
| supercell_plot_tSNE | Plot super-cell tSNE (Use supercell_DimPlot instead) Plots... |
| supercell_plot_UMAP | Plot super-cell UMAP (Use supercell_DimPlot instead) Plots... |
| supercell_prcomp | compute PCA for super-cell data (sample-weighted data) |
| supercell_purity | Compute purity of super-cells |
| supercell_rescale | Rescale supercell object |
| supercell_silhouette | Compute Silhouette index accounting for samlpe size (super... |
| supercell_tSNE | Compute tSNE of super-cells |
| supercell_UMAP | Compute UMAP of super-cells |
| supercell_VlnPlot | Violin plots |
| supercell_VlnPlot_single | Plot Violin plot for 1 feature |
