gageData
Bioc currentAuxillary data for gage package
Release Lineage
Entered 2.13 · Oct 15, 2013
Current · Requires R 4.6
Description
This is a supportive data package for the software package, gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included.
None published for Bioconductor
Call graph
Open call graph →Code intelligence has not been computed for this package yet.
Code
Structure
Lines of code
423
Files
35
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
0
Internal functions
0
Testing
Has tests
No
Test-to-code ratio
–
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
–
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.10
System requirements
–
C++ standard
–
License
GPL (>=2.0)
License flags
not SPDX, not OSI
History
Versions
26
First release
2013-12-13
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
- 5
- Examples that run
- 100%5 run in a plain check
- Exported functions with examples
- not tracked
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 100%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| bmp6 | matrix | 17,663 × 4 | No other package |
| carta.hs | list | 259 elements | 2 packages |
| go.sets.hs | list | 17,202 elements | No other package |
| go.sets.mm | list | 17,001 elements | No other package |
| go.sets.rn | list | 16,962 elements | No other package |
| go.sets.sc | list | 7,266 elements | No other package |
| go.subs.hs | list | 3 elements | No other package |
| go.subs.mm | list | 3 elements | No other package |
| go.subs.rn | list | 3 elements | No other package |
| go.subs.sc | list | 3 elements | No other package |
| gse16873.2 | matrix | 11,979 × 12 | No other package |
| gse16873.affyid | matrix | 19,940 × 12 | No other package |
| gse16873.full | matrix | 11,979 × 40 | No other package |
| hnrnp.cnts | matrix | 22,932 × 8 | No other package |
| kegg.sets.hs | list | 229 elements | No other package |
| kegg.sets.ko | list | 358 elements | No other package |
| kegg.sets.mm | list | 225 elements | No other package |
| kegg.sets.rn | list | 225 elements | No other package |
| kegg.sets.sc | list | 99 elements | No other package |
| orf2eg | vector | 6,207 elements | No other package |
| sc.gene | matrix | 6,201 × 3 | No other package |
| sigmet.idx.hs | vector | 177 elements | No other package |
| sigmet.idx.ko | vector | 288 elements | No other package |
| sigmet.idx.mm | vector | 177 elements | No other package |
| sigmet.idx.rn | vector | 177 elements | No other package |
| sigmet.idx.sc | vector | 96 elements | No other package |
Topics
Suggested by (1)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("gageData")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.