SpatialExperiment
Bioc currentS4 Class for Spatially Resolved -omics Data
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
29 5 exported
Complexity
4.5 avg / 27 max
Call network
29 nodes / 15 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
5,964
Files
71
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
31
Internal functions
24
Testing & CI
Has tests
Yes
Test-to-code ratio
0.39
testthat edition
–
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL-3
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
100%
Dep drift
9
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
- 67%
- References docs
- 0%
Topics
Depended on by (90)
Bioconductor (88)
People
- Dario Righelli author maintainer
- Helena L. Crowell author
- Nicholas J. Eagles contributor
- Davide Risso author
- Lukas M. Weber author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("SpatialExperiment")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 v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.