gep2pep
Bioc currentCreation and Analysis of Pathway Expression Profiles (PEPs)
Release Lineage
Entered 3.7 · May 1, 2018
Current · Requires R 4.6
Description
Pathway Expression Profiles (PEPs) are based on the expression of pathways (defined as sets of genes) as opposed to individual genes. This package converts gene expression profiles to PEPs and performs enrichment analysis of both pathways and experimental conditions, such as "drug set enrichment analysis" and "gene2drug" drug discovery analysis respectively.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
56 25 exported
Complexity
4.9 avg / 22 max
Call network
56 nodes / 84 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
5,625
Files
39
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
25
Internal functions
31
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.30
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
9.1%
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
17
First release
2018-04-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 27includes a package overview page
- Examples that run
- 100%25 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 15%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
1 practice detected in the Bioconductor git repository
Datasets
Topics
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("gep2pep")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.