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 dim representation
anndata_2_supercell     Convert Anndata metacell object (Metacell-2 or
                        SEACells) to Super-cell like object
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
sc_mixing_score         Compute mixing of single-cells within supercell
supercell_2_Seurat      Super-cells to Seurat object
supercell_2_sce         Super-cells to SingleCellExperiment object
supercell_DimPlot       Plot metacell 2D plot (PCA, UMAP, tSNE etc)
supercell_FindAllMarkers
                        Differential expression analysis of supep-cell
                        data. Most of the parameters are the same as in
                        Seurat FindAllMarkers (for simplicity)
supercell_FindMarkers   Differential expression analysis of supep-cell
                        data. Most of the parameters are the same as in
                        Seurat FindMarkers (for simplicity)
supercell_GE            Simplification of scRNA-seq dataset
supercell_GE_idx        Simplification of scRNA-seq dataset (old
                        version, not used since 12.02.2021)
supercell_GeneGenePlot
                        Gene-gene correlation plot
supercell_GeneGenePlot_single
                        Plot Gene-gene correlation plot for 1 feature
supercell_UMAP          Compute UMAP of super-cells
supercell_VlnPlot       Violin plots
supercell_VlnPlot_single
                        Plot Violin plot for 1 feature
supercell_assign        Assign super-cells to the most aboundant
                        cluster
supercell_cluster       Cluster super-cell data
supercell_estimate_velocity
                        Run RNAvelocity for super-cells (slightly
                        modified from
                        <https://github.com/velocyto-team/velocyto.R>)
                        Not yet adjusted for super-cell size (not
                        sample-weighted)
supercell_merge         Merging independent SuperCell objects
supercell_mergeGE       Merging metacell gene expression matrices from
                        several independent SuperCell objects
supercell_plot          Plot metacell NW
supercell_plot_GE       Plot super-cell NW colored by an expression of
                        a gene (gradient color)
supercell_plot_UMAP     Plot super-cell UMAP (Use supercell_DimPlot
                        instead) Plots super-cell UMAP (result of
                        supercell_UMAP)
supercell_plot_tSNE     Plot super-cell tSNE (Use supercell_DimPlot
                        instead) Plots super-cell tSNE (result of
                        supercell_tSNE)
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 cells size) ###
supercell_tSNE          Compute tSNE of super-cells
