Simplification of scRNA-Seq Data by Merging Together Similar Cells

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Documentation for package ‘SuperCell’ version 1.0.1

• 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