SuperCell

1.1

Simplification of scRNA-Seq Data by Merging Together Similar Cells

0packages depend

6.4Kdownloads / year

21.9%test coverage

13/13checks pass

Overview

About

Maintained by Matei TelemanFirst published 2024-09-053 releasesCRAN page ↗GitHub ↗

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 and 'WeightedCluster' doi:10.12682/lives.2296-1658.2013.24 https://mephisto.unige.ch/weightedcluster/ for weighted clustering on metacells. We also recommend installing 'scater' Bioconductor package doi:10.18129/B9.bioc.scater https://bioconductor.org/packages/release/bioc/html/scater.html.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("SuperCell", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("GfellerLab/SuperCell")

Development version from GfellerLab/SuperCell. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-supercell

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-SuperCell

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-SuperCell

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.8 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.05

21.9%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-09
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 425 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

6.4K

CRAN downloads in the past year

Rank #11,268 · ~17/day · ~530/mo

Releases R versions

Daily download trend is not available in this view yet.

27530 days

94790 days

6.4K1 year

Compare downloads with other packages →

Also on206 r2u33 autocran144 conda_forge

Repository

GitHub ↗ gfellerlab/supercell

104Stars

16Forks

5Open issues

2Open PRs

1Releases

240Commits

6Contributors

scrna-seq-datascrna-seq-analysiscoarse-grainingr-package

License GPL-3.0 · 240 commits · Last activity 2026-04-16 · +2% stars, 30d

Stars over time

2025-07-09 · 842026-07-09 · 103

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/gfellerlab/supercell on 2026-07-19.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

30 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (21)

igraph RANN corpcor weights HmiscMatrixmatrixStats plyr irlbagrDevicespatchwork ggplot2 umap entropy Rtsne dbscan scales plotfunctions proxymethodsrlang

LinkingTo (0)

none

Suggests (12)

SingleCellExperiment SummarizedExperiment cowplot scater Seurat knitr rmarkdown remotes bluster velocyto.R WeightedCluster testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 3,695 (65%)Rd 1,575 (28%)Vignettes 400 (7%)

Code characteristics

Cyclomatic complexity: 7.0 median / 34 max
Test cases: 8 / 0.05 per code line

Test coverage

Line coverage

22%

Expression

20.9%

Tests / Examples

21.9% / 0% ex

Functions

36 30 exported

Complexity

9.2 avg / 34 max

Call network

36 nodes / 18 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

36 functions

Function	Cyclo	Coverage
SCimplify_for_velocity exp	3	0%
anndata_2_supercell exp	5	0%
metacell2_anndata_2_supercell exp	2	0%
sc_mixing_score exp	3	0%
supercell_2_Seurat exp	15	0%
supercell_2_sce exp	13	0%

People & History

People (2)

Maintainer (1)

Matei Teleman

Maintainer · added in 1.1

Authors (1)

Mariia Bilous

Author

Listed in earlier versions (1)

Leonard Herault

no longer listed · 1.0 to 1.0.1

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.1Latest
2025-12-16 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.1
2024-10-25 · diff ↗
1.0
2024-09-05
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-09-05
Total releases: 3 / 2 yrs
License: GPL-3 OSI
Additional repositories: mteleman.github.io
Minimum R: ≥ 4.0.0
Bundled data: 2.5 MB / 1 file
Download size: 3.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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