Package: SuperCell 1.0

The package maintainer

SuperCell: Simplification of scRNA-seq data by merging together similar cells

Aggregates large single-cell data into metacell dataset by merging together gene expression of very similar cells.

Authors:Mariia Bilous

SuperCell_1.0.tar.gz
SuperCell_1.0.zip(r-4.7)SuperCell_1.0.zip(r-4.6)SuperCell_1.0.zip(r-4.5)
SuperCell_1.0.tgz(r-4.6-any)SuperCell_1.0.tgz(r-4.5-any)
SuperCell_1.0.tar.gz(r-4.7-any)SuperCell_1.0.tar.gz(r-4.6-any)
SuperCell_1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SuperCell/json (API)

# Install 'SuperCell' in R:
install.packages('SuperCell', repos = c('https://gfellerlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gfellerlab/supercell/issues

Datasets:

On CRAN:

Conda:

softwarecoarse-grainingscrna-seq-analysisscrna-seq-data

8.33 score 102 stars 1 packages 117 scripts 288 downloads 30 exports 165 dependencies

Last updated from:f0a041e92a. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE270
source / vignettesOK451
linux-release-x86_64NOTE259
macos-release-arm64NOTE201
macos-oldrel-arm64NOTE197
windows-develNOTE210
windows-releaseNOTE167
windows-oldrelNOTE172
wasm-releaseOK217

Exports:anndata_2_supercellbuild_knn_graphmetacell2_anndata_2_supercellsc_mixing_scoreSCimplifySCimplify_for_velocitySCimplify_from_embeddingsupercell_2_scesupercell_2_Seuratsupercell_assignsupercell_clustersupercell_DimPlotsupercell_estimate_velocitysupercell_FindAllMarkerssupercell_FindMarkerssupercell_GEsupercell_GeneGenePlotsupercell_mergesupercell_mergeGEsupercell_plotsupercell_plot_GEsupercell_plot_tSNEsupercell_plot_UMAPsupercell_prcompsupercell_puritysupercell_rescalesupercell_silhouettesupercell_tSNEsupercell_UMAPsupercell_VlnPlot

Dependencies:abindaskpassassortheadbackportsbase64encbeachmatBHBiocGenericsBiocNeighborsBiocParallelbitbit64blusterbootbroombslibcachemcheckmateclicliprclustercodetoolscolorspacecorpcorcowplotcpp11crayondata.tabledbscanDelayedArraydigestdoFuturedplyrentropyevaluatefarverfastclusterfastmapfontawesomeforcatsforeachforeignformatRFormulafsfutile.loggerfutile.optionsfuturefuture.applygdatagenericsggplot2glmnetglobalsgluegridExtragtablegtoolshavenherehighrHmischmshtmlTablehtmltoolshtmlwidgetsigraphIRangesirlbaisobanditeratorsjomojquerylibjsonliteknitrlabelinglambda.rlatticelifecyclelistenvlme4magrittrmarginsMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmicemimeminqamitmlnlmenloptrnnetnumDerivopensslordinalpanparallellypatchworkpermutepillarpkgconfigplotfunctionsplyrpngpredictionprettyunitsprogressprogressrproxypurrrR6RANNrappdirsrbibutilsRColorBrewerRcppRcppEigenRcppTOMLRdpackreadrreformulasreticulaterlangrmarkdownrpartrprojrootRSpectrarstudioapiRtsneS4ArraysS4VectorsS7sassscalesshapesnowSparseArraystringistringrsurvivalsystibbletidyrtidyselecttinytexTraMineRtzdbucminfumaputf8vctrsveganvegclustviridisLitevroomWeightedClusterweightswithrxfunXVectoryaml

Combined or independent SuperCell runs for different samples

Rendered fromb_Combined_vs_independent_sample_processing.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2022-07-18
Started: 2022-07-18

Example of the SuperCell pipeline

Rendered froma_SuperCell.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2026-02-19
Started: 2022-07-18

RNA-velocity for SuperCell

Rendered fromc_RNAvelocity_for_SuperCell.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2022-07-18
Started: 2022-07-18

Readme and manuals

Help Manual

Help pageTopics
Convert Anndata metacell object (Metacell-2 or SEACells) to Super-cell like objectanndata_2_supercell
Build kNN graphbuild_knn_graph
Build kNN graph using RANN::nn2 (used in '"build_knn_graph"')build_knn_graph_nn2
Cancer cell lines datasetcell_lines
Build kNN graph from distance (used in '"build_knn_graph"')knn_graph_from_dist
Convert Metacells (Metacell-2) to Super-cell like objectmetacell2_anndata_2_supercell
Pancreatic cell datasetpancreas
Compute mixing of single-cells within supercellsc_mixing_score
Detection of metacells with the SuperCell approachSCimplify
Construct super-cells from spliced and un-spliced matricesSCimplify_for_velocity
Detection of metacells with the SuperCell approach from low dim representationSCimplify_from_embedding
Super-cells to SingleCellExperiment objectsupercell_2_sce
Super-cells to Seurat objectsupercell_2_Seurat
Assign super-cells to the most aboundant clustersupercell_assign
Cluster super-cell datasupercell_cluster
Plot metacell 2D plot (PCA, UMAP, tSNE etc)supercell_DimPlot
Run RNAvelocity for super-cells (slightly modified from gene.relative.velocity.estimates) Not yet adjusted for super-cell size (not sample-weighted)supercell_estimate_velocity
Differential expression analysis of supep-cell data. Most of the parameters are the same as in Seurat FindAllMarkers (for simplicity)supercell_FindAllMarkers
Differential expression analysis of supep-cell data. Most of the parameters are the same as in Seurat FindMarkers (for simplicity)supercell_FindMarkers
Simplification of scRNA-seq datasetsupercell_GE
Simplification of scRNA-seq dataset (old version, not used since 12.02.2021)supercell_GE_idx
Gene-gene correlation plotsupercell_GeneGenePlot
Plot Gene-gene correlation plot for 1 featuresupercell_GeneGenePlot_single
Merging independent SuperCell objectssupercell_merge
Merging metacell gene expression matrices from several independent SuperCell objectssupercell_mergeGE
Plot metacell NWsupercell_plot
Plot super-cell NW colored by an expression of a gene (gradient color)supercell_plot_GE
Plot super-cell tSNE (Use supercell_DimPlot instead) Plots super-cell tSNE (result of supercell_tSNE)supercell_plot_tSNE
Plot super-cell UMAP (Use supercell_DimPlot instead) Plots super-cell UMAP (result of supercell_UMAP)supercell_plot_UMAP
compute PCA for super-cell data (sample-weighted data)supercell_prcomp
Compute purity of super-cellssupercell_purity
Rescale supercell objectsupercell_rescale
Compute Silhouette index accounting for samlpe size (super cells size) ###supercell_silhouette
Compute tSNE of super-cellssupercell_tSNE
Compute UMAP of super-cellssupercell_UMAP
Violin plotssupercell_VlnPlot
Plot Violin plot for 1 featuresupercell_VlnPlot_single