SpatialDecon
Bioc currentDeconvolution of mixed cells from spatial and/or bulk gene expression data
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
Using spatial or bulk gene expression data, estimates abundance of mixed cell types within each observation. Based on "Advances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data", Danaher (2022). Designed for use with the NanoString GeoMx platform, but applicable to any gene expression data.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
17 10 exported
Complexity
8.5 avg / 30 max
Call network
17 nodes / 9 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
5,593
Files
64
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
10
Internal functions
7
Testing & CI
Has tests
Yes
Test-to-code ratio
0.14
testthat edition
–
CI present
Yes
CI type
["github-actions"]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
9.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
12
First release
2020-10-27
Latest release
2026-04-28
Avg cadence
175 days
Cold removal rate
–
Dep drift
8
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
- Maddy Griswold maintainer author
- Patrick Danaher author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("SpatialDecon")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 v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.