Simplification of scRNA-Seq Data by Merging Together Similar Cells
Convert Anndata metacell object (Metacell-2 or SEACells) to Super-cell...
Build kNN graph using RANN::nn2 (used in "build_knn_graph")
Build kNN graph
Build kNN graph from distance (used in "build_knn_graph")
Convert Metacells (Metacell-2) to Super-cell like object
Compute mixing of single-cells within supercell
Construct super-cells from spliced and un-spliced matrices
Detection of metacells with the SuperCell approach from low dim repres...
Detection of metacells with the SuperCell approach
Super-cells to SingleCellExperiment object
Super-cells to Seurat object
Assign super-cells to the most aboundant cluster
Cluster super-cell data
Plot metacell 2D plot (PCA, UMAP, tSNE etc)
Run RNAvelocity for super-cells (slightly modified from [https://githu...
Differential expression analysis of supep-cell data. Most of the param...
Differential expression analysis of supep-cell data. Most of the param...
Simplification of scRNA-seq dataset (old version, not used since 12.02...
Simplification of scRNA-seq dataset
Plot Gene-gene correlation plot for 1 feature
Gene-gene correlation plot
Merging independent SuperCell objects
Merging metacell gene expression matrices from several independent Sup...
Plot super-cell NW colored by an expression of a gene (gradient color)
Plot super-cell tSNE (Use supercell_DimPlot instead) Plots super-cell ...
Plot super-cell UMAP (Use supercell_DimPlot instead) Plots super-cell ...
Plot metacell NW
compute PCA for super-cell data (sample-weighted data)
Compute purity of super-cells
Rescale supercell object
Compute Silhouette index accounting for samlpe size (super cells size)...
Compute tSNE of super-cells
Compute UMAP of super-cells
Plot Violin plot for 1 feature
Violin plots
Aggregates large single-cell data into metacell dataset by merging together gene expression of very similar cells. 'SuperCell' uses 'velocyto.R' <doi:10.1038/s41586-018-0414-6> <https://github.com/velocyto-team/velocyto.R> for RNA velocity. We also recommend installing 'scater' Bioconductor package <doi:10.18129/B9.bioc.scater> <https://bioconductor.org/packages/release/bioc/html/scater.html>.