R Observatory: Metrics for SuperCell version 1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SuperCell

1.2Package record

Simplification of scRNA-Seq Data by Merging Together Similar Cells

0packages depend

5.3Kdownloads / year

21.9%test coverage

13/13flavors OK

Overview

About

Maintained by Matei TelemanCRAN page ↗GitHub ↗Issues ↗

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-08
ERROR12 OK, 1 ERROR2026-10-06
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 6 earlier changesHide 6 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02
ERROR11 OK, 1 ERROR2026-04-25
NOTE11 OK, 3 NOTE2026-04-10
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-09
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2

READMEYes · 425 wordsVignettesYes · 2 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 36
Examples that run: 0%5 only when donttest examples are enabled (R CMD check --as-cran) · 1 hold no code
Exported functions with examples: 20%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

5.3K

CRAN downloads in the past year

Rank #5,576 · ~15/day · ~445/mo

Releases R versions

Daily download trend is not available in this view yet.

70630 days

1.5K90 days

5.3K1 year

Compare downloads with other packages →

Also on139 r2u7 autocran194 conda_forge

How downloads are counted

Repository

gfellerlab/supercell ↗Organization: GfellerLab

110Stars

15Forks

6Open issues

2Open PRs

1Releases

240Commits

6Commit identities

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

License file reads as GPL-3.0 · 240 commits · Last activity 2026-02-19 · 0% stars, 30d · The default branch showed an older version (1.0) than CRAN on 2026-10-11

Responsiveness

How these are sampled

PRs merged (all time): 84%
Median days to close, 50 most recently updated closed issues: 303
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-08 · 902026-09-15 · 110

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/gfellerlab/supercell on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Code of conduct

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

30 external dependencies (excludes base and recommended)

Installing SuperCell adds 117 packages (68 with compiled code, 95 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Matei Teleman

Maintainer since 1.1 (2025) · added in 1.1

Mariia Bilous

Author

Previously maintained by Leonard Herault (1.0 to 1.0.1).

Listed in earlier versions (1)

Leonard Herault

no longer listed · 1.0 to 1.0.1

Releases (4)

Pick two releases to compare their code metrics.

1.2Latest
record
2026-10-06 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.1
record
2025-12-16 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.1
record
2024-10-25 · diff ↗
1.0
record
2024-09-05
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-09-05
Total releases: 4 / 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

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SuperCell")

Format

Teleman, M., & Bilous, M. (2026). SuperCell: Simplification of scRNA-Seq Data by Merging Together Similar Cells (Version 1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.SuperCell

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for SuperCell version 1.2 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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