Pigengene
Bioc currentInfers biological signatures from gene expression data
Release Lineage
Entered 3.4 · Oct 18, 2016
Current · Requires R 4.6
Description
Pigengene package provides an efficient way to infer biological signatures from gene expression profiles. The signatures are independent from the underlying platform, e.g., the input can be microarray or RNA Seq data. It can even infer the signatures using data from one platform, and evaluate them on the other. Pigengene identifies the modules (clusters) of highly coexpressed genes using coexpression network analysis, summarizes the biological information of each module in an eigengene, learns a Bayesian network that models the probabilistic dependencies between modules, and builds a decision tree based on the expression of eigengenes.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
69 29 exported
Complexity
6.8 avg / 28 max
Call network
69 nodes / 141 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
7,163
Files
116
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
29
Internal functions
40
Recent export changes
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
8
Dep constraint coverage
15.4%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0.3
System requirements
–
C++ standard
–
License
GPL (>=2)
License flags
not SPDX, not OSI
History
Versions
20
First release
2016-10-17
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
9
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 35includes a package overview page
- Examples that run
- 97%33 run in a plain check · 1 hold no code
- Exported functions with examples
- 100%
- Documented parameters
- 95%
- Return-value docs
- 100%
- Help pages citing references
- 46%
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 |
|---|---|---|---|
| aml | matrix | 202 × 1,000 | No other package |
| eigengenes33 | list | 3 elements | No other package |
| mds | matrix | 164 × 1,000 | No other package |
| pigengene | pigengene | 12 elements | No other package |
Topics
Depended on by (1)
Bioconductor (1)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("Pigengene")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
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.