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 · Package record · 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.

Advisories

None published for Bioconductor

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 →

Loading call graph…

Lowest coverage

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

How coverage is measured·How the call graph is built

Code

Structure

Lines of code

4,665

Files

61

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

Has tests

Yes

Test-to-code ratio

0.11

testthat edition

–

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

In the Bioconductor 3.23 release

READMEYes · 94 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structuredCitation fileNo

Help pages: 22 (1 internal)includes a package overview page
Examples that run: 100%17 run in a plain check
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

TCGAutils Essentials HTML

How these are measured

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/waldronlab/tcgautils on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

Docs source (2)

pkgdown

GitHub Pages site

How this is detected·Detection ruleset v3 (2026-09-26)

Datasets

Bundled datasets · 5

Name	Class	Size	Also in
blca_cnaseq	data.frame	232 × 6	No other package
bt.exon_quantification	data.frame	100 × 4	No other package
clinicalNames	–	–	–
diseaseCodes	data.frame	37 × 4	No other package
sampleTypes	data.frame	22 × 3	No other package

All of TCGAutils's data objects

Topics

Software

Software › WorkflowStep

Software › WorkflowStep › Preprocessing

Software › Infrastructure › DataImport

Maintainer: Marcel Ramos

Available on

CRANr2uBioconductorautoCRANCOPR

Depended on by (5)

Bioconductor (5)

cBioPortalData glmSparseNet imageFeatureTCGA RTCGAToolbox terraTCGAdata

Suggested by (4)

CNVRanger curatedTCGAData dce IntOMICS

People

Marcel Ramos author maintainer
NCI funder
U24CA289073
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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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