SPsimSeq
Bioc currentSemi-parametric simulation tool for bulk and single-cell RNA sequencing data
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
SPsimSeq uses a specially designed exponential family for density estimation to constructs the distribution of gene expression levels from a given real RNA sequencing data (single-cell or bulk), and subsequently simulates a new dataset from the estimated marginal distributions using Gaussian-copulas to retain the dependence between genes. It allows simulation of multiple groups and batches with any required sample size and library size.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
25 3 exported
Complexity
4 avg / 23 max
Call network
25 nodes / 27 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
2,573
Files
72
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
3
Internal functions
22
Testing
Has tests
Yes
Test-to-code ratio
0.12
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
4.0
System requirements
–
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
12
First release
2020-10-27
Latest release
2026-04-28
Avg cadence
182 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
- Help pages
- 29includes a package overview page
- Examples that run
- 100%5 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 74%
- Return-value docs
- 100%
- Help pages citing references
- 14%
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/centerforstatistics-ugent/spsimseq on 2026-10-18.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| scNGP.data | – | – | – |
| zhang.data.sub | list | 2 elements | No other package |
Topics
Depended on by (1)
Bioconductor (1)
Suggested by (1)
People
- Joris Meys maintainer
- Alemu Takele Assefa author
- Stijn Hawinkel author
- Olivier Thas thesis advisor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("SPsimSeq")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.