visiumStitched
Bioc currentEnable downstream analysis of Visium capture areas stitched together with Fiji
Release Lineage
Entered 3.21 · Apr 16, 2025
Current · Requires R 4.6
Description
This package provides helper functions for working with multiple Visium capture areas that overlap each other. This package was developed along with the companion example use case data available from https://github.com/LieberInstitute/visiumStitched_brain. visiumStitched prepares SpaceRanger (10x Genomics) output files so you can stitch the images from groups of capture areas together with Fiji. Then visiumStitched builds a SpatialExperiment object with the stitched data and makes an artificial hexagonal grid enabling the seamless use of spatial clustering methods that rely on such grid to identify neighboring spots, such as PRECAST and BayesSpace. The SpatialExperiment objects created by visiumStitched are compatible with spatialLIBD, which can be used to build interactive websites for stitched SpatialExperiment objects. visiumStitched also enables casting SpatialExperiment objects as Seurat objects.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
18 8 exported
Complexity
3.7 avg / 10 max
Call network
18 nodes / 13 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
4,104
Files
44
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
8
Internal functions
10
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.26
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
4.8%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4
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
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 17 (10 internal)
- Examples that run
- 100%7 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 89%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
11 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/lieberinstitute/visiumstitched on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-04-01 · The repository has a site deploy workflow
Topics
People
- Nicholas J. Eagles author maintainer
- Leonardo Collado-Torres contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("visiumStitched")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 v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.