GeoTcgaData
Bioc currentProcessing Various Types of Data on GEO and TCGA
Release Lineage
Entered 3.17 · Apr 26, 2023
Current · Requires R 4.6
Description
Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It's easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
36 23 exported
Complexity
3.9 avg / 27 max
Call network
36 nodes / 12 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
3,497
Files
95
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
23
Internal functions
13
Testing & CI
Has tests
Yes
Test-to-code ratio
0.08
testthat edition
3
CI present
No
CI type
[]
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
4.2.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
7
First release
2023-04-25
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 87%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Erqiang Hu author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("GeoTcgaData")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 v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.