graphite
Bioc currentGRAPH Interaction from pathway Topological Environment
Release Lineage
Entered 2.9 · Nov 1, 2011
Current · Requires R 4.6
Description
Graph objects from pathway topology derived from KEGG, Panther, PathBank, PharmGKB, Reactome SMPDB and WikiPathways databases.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
83 13 exported
Complexity
2 avg / 9 max
Call network
83 nodes / 65 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
3,346
Files
43
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
13
Internal functions
69
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.44
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
8.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2
System requirements
–
C++ standard
–
License
AGPL-3
License flags
SPDX valid, OSI approved
History
Versions
30
First release
2011-10-31
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
13
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 15
- Examples that run
- 83%10 run in a plain check · 2 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 88%
- Help pages citing references
- 27%
Repository practices
4 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/sales-lab/graphite on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Topics
Depended on by (15)
Show all 19 packagesHide all 19 packages
Bioconductor (13)
Suggested by (4)
People
- Gabriele Sales maintainer
- Enrica Calura author
- Chiara Romualdi author
Cite
Cite this package
Run in R for the authors' entry:
citation("graphite")The package provides a citation file, so citation() returns the authors' own entry.
The repository also keeps a CITATION.cff.
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.