R Observatory: Metrics for imageTCGAutils version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

imageTCGAutils

Bioc current

Utility functions for working with histopathology images

v1.0.0 · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.23 · Apr 29, 2026

Current · Requires R 4.6

1.0 In 1 of 49 releases 3.23

Description

Utility functions for working with CONCH data, listing remote files. One function assigns HoverNet nuclei to ProvGigaPath tiles with a scale factor to align coordinates. Provides internal utility functions for 'imageFeatureTCGA' and most functions are not meant for end users.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

10 4 exported

Complexity

2.1 avg / 7 max

Call network

10 nodes / 7 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

839

Files

29

Compiled share

0%

Has compiled src

No

Language breakdown

R 387 (46.1%)Tests 2 (0.2%)Docs 175 (20.9%)Vignettes 275 (32.8%)

API

Exported functions

4

Internal functions

6

Recent export changes

v3.23+4 importCONCH, listHoverNet, listProvGiga +1 more

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

0%

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

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

READMEYes · 374 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

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

Topics

Software

Software › WorkflowStep

Software › WorkflowStep › Preprocessing

Depended on by (1)

Bioconductor (1)

imageFeatureTCGA

People

Ilaria Billato author maintainer
Eslam Abousamra contributor
Marcel Ramos author

At a glance

Version: 1.0.0
Category: software
License: Artistic-2.0
Requires R: ≥ 4.6
Maintainer: Ilaria Billato
Entered: 3.23 · Apr 29, 2026
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

R (>= 4.5.0)

Imports

BiocBaseUtilsBiocdata.table dplyrgrDevicesmethodsrlangS4VectorsBiocSpatialExperimentBiocSummarizedExperimentBioc

Suggests

anndataRBiocBiocStyleBiocimageFeatureTCGABiocggplot2 knitr pawsrhdf5Biocrmarkdown sfdep spdepSpatialFeatureExperimentBioctinytest

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("imageTCGAutils")

Format

Billato, I., Abousamra, E., & Ramos, M. (2026). imageTCGAutils: Utility functions for working with histopathology images (Version 1.0.0) [Computer software]. https://bioconductor.org/packages/imageTCGAutils

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 imageTCGAutils version 1.0.0 [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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