VisiumIO
Bioc currentImport Visium data from the 10X Space Ranger pipeline
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
The package allows users to readily import spatial data obtained from either the 10X website or from the Space Ranger pipeline. Supported formats include tar.gz, h5, and mtx files. Multiple files can be imported at once with *List type of functions. The package represents data mainly as SpatialExperiment objects.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
36 11 exported
Complexity
3.9 avg / 15 max
Call network
36 nodes / 33 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
3,201
Files
67
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
11
Internal functions
25
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.00
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
–
Unsafe pattern score
0
Dep constraint coverage
9.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
5
First release
2024-04-30
Latest release
2026-04-28
Avg cadence
186 days
Cold removal rate
–
Dep drift
2
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
- 100%
- References docs
- 0%
Topics
Depended on by (7)
Bioconductor (7)
People
- Marcel Ramos author maintainer
- NCI fnd
- Helena Crowell author contributor
- Estella YiXing Dong author contributor
- Dario Righelli author contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("VisiumIO")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 v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.