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.
None published for Bioconductor
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
3,495
Files
86
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
23
Internal functions
13
Testing
Has tests
Yes
Test-to-code ratio
0.08
testthat edition
3
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
- Help pages
- 30
- Examples that run
- 87%20 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran)
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- GeoTcgaData HTML
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/yulab-smu/geotcgadata on 2026-10-21.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| GSE66705_sample2 | matrix | 999 × 3 | 2 packages |
| HONGS_p_TCGAb3_75_76_77_NSP_G | data.frame | 73 × 6 | 2 packages |
| KNELT_p_TCGA_b123_131_S | data.frame | 455 × 6 | 2 packages |
| MICHE_p_TCGAb_428_429_NS | data.frame | 97 × 6 | 2 packages |
| MINAE_p_TCGA_200_202_203_S | data.frame | 468 × 6 | 2 packages |
| geneExpress | data.frame | 10,779 × 2 | 2 packages |
| gene_cov | data.frame | 27,341 × 2 | 2 packages |
| jhu-usc.H.8.l.I.TCGA-30-1714-01A-02D-0563-05.g | data.frame | 14 × 11 | 2 packages |
| jhu-usc.e.H.10.lvl-3.TCGA-30-1880-01A-01D-0652-05.g | data.frame | 14 × 11 | 2 packages |
| jhu-usc.e.H.4.lvl-3.TCGA-13-1405-01A-01D-0460-05.g | data.frame | 14 × 11 | 2 packages |
| jhu-usc.e.H.5.l.TCGA-13-1510-01A-02D-0475-05.gdc_hg38 | data.frame | 14 × 11 | 2 packages |
| kegg_liver | matrix | 100 × 150 | 2 packages |
| module | matrix | 176 × 3 | 2 packages |
| profile | matrix | 9 × 9 | 2 packages |
| ventricle | matrix | 32 × 20 | 2 packages |
3 internal objects are bundled for the package's own use and not listed here.
Topics
People
- Erqiang Hu author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("GeoTcgaData")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.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.