BioNet
Bioc currentRoutines for the functional analysis of biological networks
Release Lineage
Entered 2.7 · Oct 18, 2010
Current · Requires R 4.6
Description
This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
63 42 exported
Complexity
5.1 avg / 30 max
Call network
63 nodes / 43 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
4,792
Files
73
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
42
Internal functions
21
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
20%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.10.0
System requirements
–
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
32
First release
2010-10-18
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
5
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 44includes a package overview page
- Examples that run
- 95%39 run in a plain check · 2 never run
- Exported functions with examples
- 95%
- Documented parameters
- 99%
- Return-value docs
- 67%
- Help pages citing references
- 16%
- BioNet Tutorial PDF
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 |
|---|---|---|---|
| ALL_cons_n.txt.0 | data.frame | 5,759 × 3 | No other package |
| ALL_edges_001.txt.0 | – | – | – |
| ALL_n_resample.txt.0 | data.frame | 5,759 × 102 | No other package |
| ALL_nodes_001.txt.0 | data.frame | 5,759 × 3 | No other package |
| lymphoma_edges_001.txt.0 | data.frame | 7,755 × 3 | No other package |
| lymphoma_nodes_001.txt.0 | data.frame | 2,033 × 2 | No other package |
| pvaluesExample | matrix | 6,154 × 2 | No other package |
Topics
Depended on by (3)
Bioconductor (3)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("BioNet")The package provides a citation file, so citation() returns the authors' own entry.
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.