TCGAbiolinks
Bioc currentTCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
Release Lineage
Entered 3.2 · Oct 14, 2015
Current · Requires R 4.6
Description
The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
137 57 exported
Complexity
6.9 avg / 60 max
Call network
137 nodes / 152 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
20,843
Files
187
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
57
Internal functions
79
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.08
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
21
Dep constraint coverage
27.6%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
–
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
22
First release
2016-04-02
Latest release
2026-04-28
Avg cadence
176 days
Cold removal rate
100%
Dep drift
80
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 94 (28 internal)includes a package overview page
- Examples that run
- 69%38 run in a plain check · 17 never run
- Exported functions with examples
- 84%
- Documented parameters
- 98%
- Return-value docs
- 91%
- Help pages citing references
- 0%
- 7. Analyzing and visualizing TCGA data HTML
- 8. Case Studies HTML
- 10. Classifiers HTML
- 4. Clinical data HTML
- 3. Downloading and preparing files for analysis HTML
- 10. TCGAbiolinks_Extension HTML
- 1. Introduction HTML
- 5. Mutation data HTML
- 2. Searching GDC database HTML
- 11. Stemness score HTML
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Repository practices
4 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/bioinformaticsfmrp/tcgabiolinks on 2026-10-21.
GitHub Pages site last deployed 2020-09-22
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| DE_PCBC_stemSig | vector | 12,956 elements | No other package |
| EB_PCBC_stemSig | vector | 12,956 elements | No other package |
| ECTO_PCBC_stemSig | vector | 12,956 elements | No other package |
| MESO_PCBC_stemSig | vector | 12,956 elements | No other package |
| SC_PCBC_stemSig | vector | 12,956 elements | No other package |
| TabSubtypesCol_merged | data.frame | 4,768 × 3 | No other package |
| Tumor.purity | data.frame | 9,364 × 7 | No other package |
| bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf | tibble | 3,555 × 34 | No other package |
| chol_maf | – | – | – |
| clinical.biotab | list | 7 elements | No other package |
| dataBRCA | data.frame | 20,530 × 10 | No other package |
| dataDEGsFiltLevel | data.frame | 3,649 × 6 | No other package |
| dataREAD | – | – | – |
| dataREAD_df | data.frame | 20,531 × 2 | No other package |
| gbm.exp.harmonized | – | – | – |
| gbm.exp.legacy | – | – | – |
| geneInfo | matrix | 20,531 × 3 | 2 packages |
| geneInfoHT | data.frame | 68,016 × 2 | No other package |
| met.gbm.27k | – | – | – |
| msi_results | data.frame | 2 × 4 | No other package |
| tabSurvKMcompleteDEGs | data.frame | 200 × 7 | No other package |
39 internal objects are bundled for the package's own use and not listed here.
Topics
Depended on by (8)
Show all 13 packagesHide all 13 packages
Bioconductor (8)
Suggested by (5)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("TCGAbiolinks")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/nar/gkv1507.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.