R Observatory: Metrics for XeniumIO version 1.4.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

XeniumIO

Bioc current

Import and represent Xenium data from the 10X Xenium Analyzer

v1.4.0 · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.21 · Apr 16, 2025

Current · Requires R 4.6

1.0 In 3 of 49 releases 3.23

Description

The package allows users to readily import spatial data obtained from the 10X Xenium Analyzer pipeline. Supported formats include 'parquet', 'h5', and 'mtx' files. The package mainly represents data as SpatialExperiment objects.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

12 2 exported

Complexity

3.1 avg / 9 max

Call network

12 nodes / 8 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

758

Files

19

Compiled share

0%

Has compiled src

No

Language breakdown

R 334 (44.1%)Tests 2 (0.3%)Docs 199 (26.3%)Vignettes 223 (29.4%)

API

Exported functions

2

Internal functions

10

Recent export changes

v3.21+2 TENxXenium, XeniumFile

Testing & CI

Has tests

Yes

Test-to-code ratio

0.01

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

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

READMEYes · 888 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Topics

Software

Software › Infrastructure

Software › Infrastructure › DataImport

Software › Technology › SingleCell

Software › Technology › Spatial

People

Marcel Ramos author maintainer
NCI fnd
Estella Dong contributor
Dario Righelli contributor

At a glance

Version: 1.4.0
Category: software
License: Artistic-2.0
Requires R: ≥ 4.6
Maintainer: Marcel Ramos
Entered: 3.21 · Apr 16, 2025
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

TENxIOBiocR (>= 4.5.0)

Imports

BiocBaseUtilsBiocBiocGenericsBiocBiocIOBiocjsonlitemethodsS4VectorsBiocSingleCellExperimentBiocSpatialExperimentBiocSummarizedExperimentBiocVisiumIO (>= 1.7.5)Bioc

Suggests

arrowBiocFileCacheBiocBiocStyleBiocknitr rmarkdown tinytest

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("XeniumIO")

Format

Ramos, M., NCI, Dong, E., & Righelli, D. (2026). XeniumIO: Import and represent Xenium data from the 10X Xenium Analyzer (Version 1.4.0) [Computer software]. https://bioconductor.org/packages/XeniumIO

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.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for XeniumIO version 1.4.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

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.

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