compcodeR
Bioc currentRNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
Release Lineage
Entered 2.14 · Apr 14, 2014
Current · Requires R 4.6
Description
This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data. Finally, it provides convenient interfaces to several packages for performing the differential expression analysis. These can also be used as templates for setting up and running a user-defined differential analysis workflow within the framework of the package.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
103 36 exported
Complexity
7.2 avg / 77 max
Call network
103 nodes / 115 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
15,791
Files
132
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
36
Internal functions
66
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.38
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
3
Dep constraint coverage
7.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0
System requirements
–
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
25
First release
2014-04-11
Latest release
2026-09-10
Avg cadence
186 days
Cold removal rate
100%
Dep drift
14
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 66 (26 internal)includes a package overview page
- Examples that run
- 100%39 run in a plain check (2 of them under a condition)
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 61%
- Help pages citing references
- 27%
- compcodeR HTML
- phylocompcodeR HTML
Repository practices
5 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/csoneson/compcoder on 2026-10-11.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-09-10 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| Pickrell.Cheung.Mu.Phi.Estimates | list | 2 elements | No other package |
| Stern2018.Length.Mu.Phi.Estimates | list | 2 elements | No other package |
Topics
People
- Charlotte Soneson author maintainer
- Paul Bastide author
- Mélina Gallopin author
Cite
Cite this package
Run in R for the authors' entry:
citation("compcodeR")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 v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.