NetPathMiner
Bioc currentNetPathMiner for Biological Network Construction, Path Mining and Visualization
Release Lineage
Entered 2.14 · Apr 14, 2014
Current · Requires R 4.6
Description
NetPathMiner is a general framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations, metabolic, reaction and gene representations. NetPathMiner finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
115 44 exported
Complexity
5.4 avg / 41 max
Call network
115 nodes / 149 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
9,646
Files
81
Compiled share
21.9%
Has compiled src
Yes
Language breakdown
API
Exported functions
44
Internal functions
32
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
18.2%
Unsafe pattern score
0
Dep constraint coverage
100%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.0.2
System requirements
2 externallibxml2, libSBML (>= 5.5)
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
25
First release
2014-05-09
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
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
- 41includes a package overview page
- Examples that run
- 100%38 run in a plain check (1 of them under a condition)
- Exported functions with examples
- 94%
- Documented parameters
- 99%
- Return-value docs
- 97%
- Help pages citing references
- 5%
Repository practices
9 development-tooling and community-health practices detected across 5 families in the upstream repository
Checks run against github.com/ahmohamed/netpathminer on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2024-11-27 · The repository has a site deploy workflow
Show all practicesHide 1 practice
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| bridge | data.frame | 131 × 11 | No other package |
| bridge.organisms | vector | 30 elements | No other package |
| bridge.web | vector | 1 element | No other package |
| ex_biopax | biopax | 7 elements | No other package |
| ex_kgml_sig | igraph | 170 edges | No other package |
| ex_microarray | matrix | 281 × 126 | No other package |
| ex_sbml | igraph | 662 edges | No other package |
| memory.err | vector | 0 elements | 6 packages |
| small.comp.ls | data.frame | 135 × 6 | No other package |
Topics
Depended on by (1)
Bioconductor (1)
People
- Ahmed Mohamed author maintainer
- Tim Hancock author
- Tim Hancock author
Cite
Cite this package
Run in R for the authors' entry:
citation("NetPathMiner")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 v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.