spatialDE
Bioc currentR wrapper for SpatialDE
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
21 7 exported
Complexity
1.7 avg / 8 max
Call network
21 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
2,525
Files
41
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
11
Internal functions
14
Testing
Has tests
Yes
Test-to-code ratio
0.16
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
8.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
10
First release
2021-10-26
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 14 (1 internal)
- 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
- 71%
Repository practices
5 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/sales-lab/spatialde on 2026-10-25.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| MOB_sample_info | data.frame | 260 × 3 | No other package |
| Rep11_MOB_0 | matrix | 16,218 × 262 | No other package |
Topics
Suggested by (1)
People
- Gabriele Sales maintainer
- Davide Corso author
- Milan Malfait author
- Lambda Moses author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("spatialDE")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 v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.