KEGGgraph
Bioc currentKEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
Release Lineage
Entered 2.4 · Apr 21, 2009
Current · Requires R 4.6
Description
KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
56 34 exported
Complexity
2.5 avg / 9 max
Call network
56 nodes / 38 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
4,483
Files
98
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
46
Internal functions
21
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.17
testthat edition
–
Docs
Roxygen coverage
76.1%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
25%
Unsafe pattern score
0
Dep constraint coverage
16.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
–
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
35
First release
2009-06-10
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
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
- 58
- Examples that run
- 100%41 run in a plain check
- Exported functions with examples
- 77%
- Documented parameters
- 100%
- Return-value docs
- 97%
- Help pages citing references
- 45%
Repository practices
Repository github.com/accio/research is linked, but repository-practices checks have not run for it yet.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| KEGGEdgeSubtype | data.frame | 17 × 11 | No other package |
| KEGGEdgeType | data.frame | 5 × 2 | No other package |
| KEGGNodeType | data.frame | 6 × 2 | No other package |
| KEGGPATHID2NAME | – | – | – |
| top | data.frame | 20,111 × 7 | No other package |
Topics
Depended on by (13)
Show all 18 packagesHide all 18 packages
Bioconductor (13)
Suggested by (5)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("KEGGgraph")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 v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.