SpatialArtifacts
Bioc currentIdentification and Classification of Spatial Artifacts in Visium and Visium HD Data
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
SpatialArtifacts provides a data-driven two-step workflow to identify, classify, and handle spatial artifacts in spatial transcriptomics data. The package combines median absolute deviation (MAD)-based outlier detection with morphological image processing (fill, outline, and star patterns) to detect edge and interior artifacts. It supports multiple platforms including 10x Genomics Visium (standard and HD), allowing for consistent quality control across different spatial resolutions.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
18 9 exported
Complexity
9.1 avg / 34 max
Call network
18 nodes / 11 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
3,921
Files
33
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
9
Internal functions
6
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.18
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
4 externalquarto, GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0)
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-04-28
Latest release
2026-04-28
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 11includes a package overview page
- Examples that run
- 100%10 run in a plain check (1 of them under a condition)
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 9%
Repository practices
5 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/cambridgecat13/spatialartifacts on 2026-10-21.
GitHub Pages site last deployed 2026-05-04 · The repository has a site deploy workflow
Datasets
Topics
People
- Harriet Jiali He author maintainer
- Stephanie C. Hicks author funder
- Jacqueline R. Thompson author
- Michael Totty author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("SpatialArtifacts")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.