R Observatory: Metrics for SCORPION version 1.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SCORPION

1.3.2

Single Cell Oriented Reconstruction of PANDA Individually Optimized Networks

0packages depend

4.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Daniel OsorioFirst published 2022-09-218 releasesCRAN page ↗GitHub ↗

Constructs cell-type–specific gene regulatory networks from single-cell RNA-sequencing data. The method implements the SCORPION algorithm, which first aggregates individual cells into super-cells and then applies PANDA (Passing Attributes between Networks for Data Assimilation) to infer transcription factor–target regulatory relationships. It also provides statistical methods for differential edge analysis.

Install

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

install.packages("SCORPION", 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("kuijjerlab/SCORPION")

Development version from kuijjerlab/SCORPION. 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-scorpion

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-SCORPION

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-SCORPION

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

Health

CRAN checks

13OK

Slowest check: 2.3 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

10

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 40%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

4.6K

CRAN downloads in the past year

Rank #7,203 · ~13/day · ~382/mo

Releases R versions

Daily download trend is not available in this view yet.

21030 days

1.2K90 days

4.6K1 year

Compare downloads with other packages →

Also on157 r2u17 autocran

Repository

GitHub ↗ kuijjerlab/scorpion

28Stars

4Forks

1Open issues

0Open PRs

7Releases

179Commits

3Contributors

gene-regulatory-networksingle-celltranscription-factorstranscriptomicsprotein-protein-interactioncomparative-edge-analysiscell-type-specificpopulation-comparison

License GPL-3.0 · 179 commits · Last activity 2026-08-16 · +3.7% stars, 30d

Stars over time

2026-07-14 · 272026-07-23 · 28

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/kuijjerlab/scorpion on 2026-08-16.

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (10)

climethodsirlba igraph RANNMatrixpbapply dplyr furrr future

LinkingTo (0)

none

Suggests (2)

RhpcBLASctl testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Daniel Osorio

Author, Maintainer

Authors (2)

Daniel Osorio

Author, Maintainer

Marieke L. Kuijjer

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.3.2Latest
2026-03-10 · current release · diff ↗
1.3.1
2026-02-12 · diff ↗
1.3.0
2026-02-05 · diff ↗
1.2.0
2025-09-24 · diff ↗
1.1.0
2025-08-25 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.2
2024-05-29 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.0.1
2022-09-22 · diff ↗
1.0.0
2022-09-21
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-09-21
Total releases: 8 / 4 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 706 KB / 2 files
Download size: 1.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SCORPION")

Format

Osorio, D., & Kuijjer, M. L. (2026). SCORPION: Single Cell Oriented Reconstruction of PANDA Individually Optimized Networks (Version 1.3.2) [Computer software]. https://doi.org/10.32614/CRAN.package.SCORPION

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 SCORPION version 1.3.2 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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