genefu
Bioc currentComputation of Gene Expression-Based Signatures in Breast Cancer
Release Lineage
Entered 2.8 · Apr 14, 2011
Current · Requires R 4.6
Description
This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
51 50 exported
Complexity
8.1 avg / 33 max
Call network
51 nodes / 44 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
12,724
Files
194
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
50
Internal functions
0
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
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
4.1
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
31
First release
2011-05-19
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
100%
Dep drift
10
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 77 (1 internal)includes a package overview page
- Examples that run
- 100%45 run in a plain check
- Exported functions with examples
- 90%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 82%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
2 practices detected in the Bioconductor git repository
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| T.E.9CELL-LINE | – | – | – |
| annot.expos | data.frame | 966 × 7 | 2 packages |
| annot.nkis | data.frame | 922 × 7 | 2 packages |
| annot.vdxs | data.frame | 966 × 7 | 2 packages |
| bentink2012_angiogenic | data.frame | 100 × 8 | No other package |
| claudinLowData | list | 6 elements | No other package |
| crijns2009_sig | data.frame | 86 × 2 | No other package |
| data.expos | matrix | 353 × 966 | No other package |
| data.nkis | matrix | 150 × 922 | 2 packages |
| data.vdxs | matrix | 150 × 966 | 2 packages |
| demo.expos | data.frame | 353 × 10 | No other package |
| demo.nkis | data.frame | 150 × 19 | 2 packages |
| demo.vdxs | data.frame | 150 × 16 | 2 packages |
| desmedt2008_genemodules | data.frame | 913 × 7 | 2 packages |
| filipits2011_sig_endopredict | data.frame | 11 × 7 | No other package |
| haibekains2009_sig_genius | data.frame | 314 × 6 | 2 packages |
| loi2008_tamr13 | data.frame | 239 × 9 | 2 packages |
| loi2010_pik3cags | data.frame | 278 × 3 | 2 packages |
| mod1 | list | 7 elements | 2 packages |
| mod2 | list | 3 elements | 2 packages |
| modelOvcAngiogenic | list | 4 elements | No other package |
| paik2004_sig_oncotypedx | data.frame | 21 × 5 | 2 packages |
| pam50 | list | 7 elements | No other package |
| pam50.robust | list | 7 elements | No other package |
| pam50.scale | list | 7 elements | No other package |
| pam50_model | data.frame | 50 × 1 | 2 packages |
| scmgene.robust | list | 4 elements | No other package |
| scmgene_robust_model | data.frame | 5 × 1 | 2 packages |
| scmod1.robust | list | 4 elements | No other package |
| scmod1_robust_model | data.frame | 728 × 1 | 2 packages |
| scmod2.robust | list | 4 elements | No other package |
| scmod2_robust_model | data.frame | 663 × 1 | No other package |
| sig.endoPredict | data.frame | 11 × 7 | No other package |
| sig.gene70 | data.frame | 70 × 9 | 2 packages |
| sig.gene76 | data.frame | 76 × 10 | 2 packages |
| sig.genius | list | 3 elements | 2 packages |
| sig.ggi | data.frame | 128 × 9 | 2 packages |
| sig.oncotypedx | data.frame | 21 × 5 | 2 packages |
| sig.pik3cags | data.frame | 278 × 3 | 2 packages |
| sig.tamr13 | list | 11 elements | 2 packages |
| sigOvcAngiogenic | data.frame | 100 × 13 | No other package |
| sigOvcCrijns | data.frame | 86 × 12 | No other package |
| sigOvcSpentzos | data.frame | 17 × 13 | No other package |
| sigOvcTCGA | data.frame | 193 × 14 | No other package |
| sigOvcYoshihara | data.frame | 88 × 13 | No other package |
| sotiriou2006_sig_ggi | data.frame | 128 × 9 | 2 packages |
| spentzos2011_sig | data.frame | 17 × 4 | No other package |
| ssp2003 | list | 7 elements | No other package |
| ssp2003.robust | list | 7 elements | No other package |
| ssp2003.scale | list | 7 elements | No other package |
| ssp2003_model | data.frame | 500 × 1 | 2 packages |
| ssp2006 | list | 7 elements | No other package |
| ssp2006.robust | list | 7 elements | No other package |
| ssp2006.scale | list | 7 elements | No other package |
| ssp2006_model | data.frame | 306 × 1 | 2 packages |
| tcga2011_sig | data.frame | 193 × 7 | No other package |
| veer2002_sig_gene70 | data.frame | 70 × 9 | 2 packages |
| wang2005_sig_gene76 | data.frame | 76 × 10 | 2 packages |
| wirapati2008_genemodules | data.frame | 663 × 10 | 2 packages |
| yoshihara2010_sig | data.frame | 88 × 4 | No other package |
Topics
Depended on by (3)
Bioconductor (3)
People
- Benjamin Haibe-Kains author maintainer
- Aleix Prat author
- Christopher Eeles contributor
- Deena M.A. Gendoo author
- Jermiah Joseph contributor
- Joel S Parker author
- Laia Pare author
- Markus S. Schroeder author
- Natchar Ratanasirigulchai author
- Nikta Feizi contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("genefu")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 v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.