scGraphVerse
Bioc currentscGraphVerse: A Gene Network Analysis Package
Release Lineage
Entered 3.22 · Oct 30, 2025
Current · Requires R 4.6
Description
A package for inferring, comparing, and visualizing gene networks from single-cell RNA sequencing data. It integrates multiple methods (GENIE3, GRNBoost2, ZILGM, PCzinb, and JRF) for robust network inference, supports consensus building across methods or datasets, and provides tools for evaluating regulatory structure and community similarity. GRNBoost2 requires Python package 'arboreto' which can be installed using init_py(install_missing = TRUE). This package includes adapted functions from ZILGM (Park et al., 2021), JRF (Petralia et al., 2015), and learn2count (Nguyen et al. 2023) packages with proper attribution under GPL-2 license.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
155 26 exported
Complexity
5 avg / 50 max
Call network
155 nodes / 151 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
16,618
Files
100
Compiled share
5.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
26
Internal functions
121
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.52
testthat edition
–
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
25%
Unsafe pattern score
0
Dep constraint coverage
3.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
2
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
2
First release
2025-10-29
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Francesco Cecere author maintainer
- Claudia Angelini author fnd
- Annamaria Carissimo author
- Daniela De Canditiis author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("scGraphVerse")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.
From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.