R Observatory: Metrics for SCORPION version 1.3.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SCORPION

1.3.4Package record

Single Cell Oriented Reconstruction of PANDA Individually Optimized Networks

0packages depend

5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Daniel OsorioCRAN page ↗GitHub ↗Issues ↗

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. 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-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). 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: 2.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.4

README· In the repository, left out of the releaseVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 13 (5 internal)
Examples that run: 29%2 run in a plain check · 5 never run
Exported functions with examples: 86%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

5K

CRAN downloads in the past year

Rank #6,270 · ~14/day · ~416/mo

Releases R versions

Daily download trend is not available in this view yet.

64830 days

1.3K90 days

5K1 year

Compare downloads with other packages →

Also on152 r2u8 autocran

How downloads are counted

Repository

kuijjerlab/scorpion ↗Organization: kuijjerlab

28Stars

5Forks

1Open issues

0Open PRs

9Releases

194Commits

3Commit identities

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

License file reads as GPL-3.0 · 194 commits · Last activity 2026-09-29 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 18
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-07-14 · 272026-07-23 · 28

How these are measured

PracticesBeta

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

Checks run against github.com/kuijjerlab/scorpion 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

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing SCORPION adds 27 packages (15 with compiled code, 13 MB of source tarballs). Heaviest: igraph 4.8 MB, vctrs 1.0 MB, dplyr 902 KB.

Depends (1)

R >= 3.5.0

Imports (10)

climethodsirlba igraph RANNMatrixpbapply dplyr furrr future

LinkingTo (0)

none

Suggests (6)

RhpcBLASctl testthat mori circlize biomaRt fgsea

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)

Daniel Osorio

Author, Maintainer since 1.0.0 (2022)

Marieke L. Kuijjer

Author

Releases (10)

Pick two releases to compare their code metrics.

1.3.4Latest
record
2026-09-21 · current release · diff ↗
1.3.3
record
2026-09-02 · diff ↗ ·
added 3 exports
circosEdges, enrichEdges, maEdges
R
R 4.6.0 released · 2026-04-24
1.3.2
record
2026-03-10 · diff ↗
1.3.1
record
2026-02-12 · diff ↗
1.3.0
record
2026-02-05 · diff ↗ ·
added 3 exports
regressEdges, runSCORPION, testEdges
1.2.0
record
2025-09-24 · diff ↗
1.1.0
record
2025-08-25 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.2
record
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
record
2022-09-22 · diff ↗
1.0.0
record
2022-09-21
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-09-21
Total releases: 10 / 4 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 705 KB / 2 files
Download size: 1.5 MB

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 1.3.4) [Computer software]. https://doi.org/10.32614/CRAN.package.SCORPION

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 SCORPION version 1.3.4 [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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