RTCGA
Bioc currentThe Cancer Genome Atlas Data Integration
Release Lineage
Entered 3.2 · Oct 14, 2015
Current · Requires R 4.6
Description
The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients' treatment. Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
28 15 exported
Complexity
3.1 avg / 16 max
Call network
28 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
4,206
Files
117
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
15
Internal functions
13
Testing & CI
Has tests
Yes
Test-to-code ratio
0.04
testthat edition
–
CI present
Yes
CI type
["travis"]
PR gated
No
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
3.3.0
System requirements
–
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
22
First release
2016-01-18
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
12
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 75%
- Documented parameters
- 93%
- Return-value docs
- 50%
- References docs
- 0%
Topics
Depended on by (9)
People
- Marcin Kosinski author maintainer
- Przemyslaw Biecek contributor
- Witold Chodor contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("RTCGA")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.
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.