DifferentialRegulation
Bioc currentDifferentially regulated genes from scRNA-seq data
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
DifferentialRegulation is a method for detecting differentially regulated genes between two groups of samples (e.g., healthy vs. disease, or treated vs. untreated samples), by targeting differences in the balance of spliced and unspliced mRNA abundances, obtained from single-cell RNA-sequencing (scRNA-seq) data. From a mathematical point of view, DifferentialRegulation accounts for the sample-to-sample variability, and embeds multiple samples in a Bayesian hierarchical model. Furthermore, our method also deals with two major sources of mapping uncertainty: i) 'ambiguous' reads, compatible with both spliced and unspliced versions of a gene, and ii) reads mapping to multiple genes. In particular, ambiguous reads are treated separately from spliced and unsplced reads, while reads that are compatible with multiple genes are allocated to the gene of origin. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques (Metropolis-within-Gibbs).
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
37 11 exported
Complexity
6.8 avg / 18 max
Call network
37 nodes / 17 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
5,639
Files
90
Compiled share
16.9%
Has compiled src
Yes
Language breakdown
API
Exported functions
11
Internal functions
13
Testing
Has tests
Yes
Test-to-code ratio
0.03
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
System requirements
1 externalC++17
C++ standard
C++17
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-07-25
Latest release
2026-04-28
Avg cadence
180 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 12includes a package overview page
- Examples that run
- 100%11 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/simonetiberi/differentialregulation on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| DF_cell_types | data.frame | 3,493 × 2 | No other package |
Topics
People
- Simone Tiberi author maintainer
- Charlotte Soneson author
Cite
Cite this package
Run in R for the authors' entry:
citation("DifferentialRegulation")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/biostatistics/kxae017.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.