scDesign3
Bioc currentA unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics
Release Lineage
Entered 3.18 · Oct 25, 2023
Current · Requires R 4.6
Description
We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data, scDesign3 infers biologically meaningful parameters; assesses the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations; and generates in silico negative and positive controls for benchmarking computational tools.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
38 13 exported
Complexity
9.7 avg / 59 max
Call network
38 nodes / 31 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
5,653
Files
43
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
13
Internal functions
25
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.04
testthat edition
3
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
6
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
6
First release
2024-01-12
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
3
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
Depended on by (1)
Bioconductor (1)
People
- Dongyuan Song author maintainer
- Chenxin Jiang author
- Qingyang Wang author
Cite
Cite this package
Start here. This is the citation for the package itself.
citation("scDesign3")Bioconductor packages have no CRAN DOI. The package landing page is https://bioconductor.org/packages/scDesign3.
BibTeX, derived from DESCRIPTION
@Manual{scDesign3,
title = {scDesign3: A unified framework of realistic in silico data generation and
statistical model inference for single-cell and spatial omics},
author = {Song, Dongyuan and Jiang, Chenxin and Wang, Qingyang},
year = {2026},
note = {R package version 1.10.0},
url = {https://bioconductor.org/packages/scDesign3}
}Derived from the package DESCRIPTION, not from a citation file the authors wrote. If they publish one later, prefer it.
This is the citation for the package. It is not a citation for the R Observatory.
Cite this page
Use this when the claim is about a measurement on this page.
BibTeX
@misc{robservatoryscDesign3,
author = {Balamuta, James Joseph},
title = {{R} {Observatory}: Metrics for {scDesign3} version 1.10.0},
year = {2026},
publisher = {HJJB, LLC},
url = {https://r-observatory.thecoatlessprofessor.com/bioc/scDesign3},
note = {Data set. Data release v2026-08-05}
}APA
Balamuta, J. J. (2026). R Observatory: Metrics for scDesign3 version 1.10.0 [Data set]. HJJB, LLC. Data release v2026-08-05. https://r-observatory.thecoatlessprofessor.com/bioc/scDesign3RIS
TY - DATA
AU - Balamuta, James Joseph
TI - R Observatory: Metrics for scDesign3 version 1.10.0
PY - 2026
PB - HJJB, LLC
N1 - Data release v2026-08-05
UR - https://r-observatory.thecoatlessprofessor.com/bioc/scDesign3
ER - In prose
These package metrics were obtained from the R Observatory (Balamuta, 2026), data release v2026-08-05, https://r-observatory.thecoatlessprofessor.com/bioc/scDesign3.Bound to data release v2026-08-05, which is what makes the numbers on this page reproducible. See how to cite.