R Observatory: Metrics for TCGAutils version 1.32.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TCGAutils

Bioc current

TCGA utility functions for data management

v1.32.2 · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.7 · May 1, 2018

Current · Requires R 4.6

1.0 In 17 of 49 releases 3.23

Description

A suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

80 32 exported

Complexity

3.1 avg / 12 max

Call network

80 nodes / 78 edges

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

Call graph

Open call graph →

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Lowest coverage

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

Code

Structure

Lines of code

4,665

Files

64

Compiled share

0%

Has compiled src

No

Language breakdown

R 2,571 (55.1%)Tests 289 (6.2%)Docs 1,241 (26.6%)Vignettes 564 (12.1%)

API

Exported functions

32

Internal functions

46

Recent export changes

v3.9+3 CpGtoRanges, getFileName, trimColData −1 getFileNames

v3.8+8 UUIDtoUUID, filenameToBarcode, imputeAssay +5 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.11

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

17

First release

2018-06-18

Latest release

2026-07-02

Avg cadence

186 days

Cold removal rate

66.7%

Dep drift

6

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 94 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Topics

Software

Software › WorkflowStep

Software › WorkflowStep › Preprocessing

Software › Infrastructure › DataImport

Depended on by (9)

Bioconductor (9)

cBioPortalData CNVRanger glmSparseNet imageFeatureTCGA RTCGAToolbox terraTCGAdata curatedTCGAData dce IntOMICS

People

Marcel Ramos author maintainer
NCI fnd
Sean Davis contributor
Lucas Schiffer author
Levi Waldron author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("TCGAutils")

Format

Ramos, M., NCI, Davis, S., Schiffer, L., & Waldron, L. (2026). TCGAutils: TCGA utility functions for data management (Version 1.32.2) [Computer software]. https://bioconductor.org/packages/TCGAutils

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 TCGAutils version 1.32.2 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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