Release Lineage
Entered 2.8 · Apr 14, 2011
Current · Requires R 4.6
Description
Pathway analysis based on p-values associated to genes from a genes expression analysis of interest. Utility functions enable to extract pathways from the Gene Ontology Biological Process (GOBP), Molecular Function (GOMF) and Cellular Component (GOCC), Kyoto Encyclopedia of Genes of Genomes (KEGG) and Reactome databases. Methodology, and helper functions to display the results as a table, barplot of pathway significance, Gene Ontology graph and pathway significance are available.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
21 6 exported
Complexity
5.9 avg / 20 max
Call network
21 nodes / 17 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
2,128
Files
30
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
6
Internal functions
15
Testing & CI
Has tests
Yes
Test-to-code ratio
0.10
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
31
First release
2011-04-14
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
100%
Dep drift
8
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 13%
Topics
Depended on by (3)
CRAN (1)
People
- Laure Cougnaud maintainer
- Dhammika Amaratunga contributor
- Javier Cabrera contributor
- Tine Casneuf contributor
- An De Bondt author
- Katarzyna Gorczak contributor
- Willem Ligtenberg contributor
- Nandini Raghavan author
- Tobias Verbeke author
Cite
Cite this package
Run in R for the authors' preferred citation:
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Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
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