SpatialExperimentIO
Bioc currentRead in Xenium, CosMx, MERSCOPE or STARmapPLUS data as SpatialExperiment object
Release Lineage
Entered 3.21 · Apr 16, 2025
Current · Requires R 4.6
Description
Read in imaging-based spatial transcriptomics technology data. Current available modules are for Xenium by 10X Genomics, CosMx by Nanostring, MERSCOPE by Vizgen, or STARmapPLUS from Broad Institute. You can choose to read the data in as a SpatialExperiment or a SingleCellExperiment object.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
10 9 exported
Complexity
5.3 avg / 14 max
Call network
10 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
2,461
Files
59
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
9
Internal functions
1
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.49
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
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
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
3
First release
2025-04-15
Latest release
2026-04-28
Avg cadence
189 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
- 90%
- Documented parameters
- 99%
- Return-value docs
- 100%
- References docs
- 0%
Topics
Depended on by (4)
Bioconductor (4)
People
- Yixing E. Dong author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("SpatialExperimentIO")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.