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.
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
76
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
3
Internal functions
22
Testing & CI
Has tests
Yes
Test-to-code ratio
0.12
testthat edition
–
CI present
No
CI type
[]
PR gated
No
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
- Examples that run
- 100%
- Documented parameters
- 74%
- Return-value docs
- 100%
- References docs
- 14%
Topics
Depended on by (2)
Bioconductor (2)
People
- Joris Meys maintainer
- Alemu Takele Assefa author
- Stijn Hawinkel author
- Olivier Thas ths
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("SPsimSeq")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 v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.