# Simplification of scRNA-Seq Data by Merging Together Similar Cells

## Documentation for package ‘SuperCell’ version 1.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
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
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 <https://github.com/velocyto-team/velocyto.R>) Not yet adjusted for super-cell size (not sample-weighted)
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_GeneGenePlot | Gene-gene correlation plot
supercell_GeneGenePlot_single | Plot Gene-gene correlation plot for 1 feature
supercell_GE_idx | Simplification of scRNA-seq dataset (old version, not used since 12.02.2021)
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_tSNE | Plot super-cell tSNE (Use supercell_DimPlot instead) Plots super-cell tSNE (result of supercell_tSNE)
supercell_plot_UMAP | Plot super-cell UMAP (Use supercell_DimPlot instead) Plots super-cell UMAP (result of supercell_UMAP)
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
supercell_UMAP | Compute UMAP of super-cells
supercell_VlnPlot | Violin plots
supercell_VlnPlot_single | Plot Violin plot for 1 feature