curatedTCGAData
Bioc currentCurated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
18 1 exported
Complexity
2.2 avg / 10 max
Call network
18 nodes / 16 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
16,563
Files
126
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
1
Internal functions
17
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.06
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
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
18
First release
2017-11-13
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
4
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 103includes a package overview page
- Examples that run
- 100%2 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0% with a bibliography file
- curatedTCGAData HTML
Repository practices
6 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/waldronlab/curatedtcgadata on 2026-10-11.
GitHub Pages site
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| metadata | data.frame | 2,845 × 17 | No other package |
1 internal object is bundled for the package's own use and not listed here.
Topics
Depended on by (3)
Bioconductor (3)
Suggested by (8)
People
- Marcel Ramos author maintainer
-
NCI
funder
U24CA289073
- Ludwig Geistlinger contributor
- Martin Morgan contributor
- Valerie Obenchain contributor
- Lucas Schiffer contributor
- Levi Waldron contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("curatedTCGAData")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1200/cci.19.00119.
The repository also keeps a CITATION.cff.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.