DEGraph
Bioc currentTwo-sample tests on a graph
Release Lineage
Entered 2.7 · Oct 18, 2010
Current · Requires R 4.6
Description
DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches which first test individual genes, then test gene sets for enrichment in differentially expressed genes. These recent methods take into account the topology of the network to yield more powerful detection procedures. DEGraph provides methods to easily test all KEGG pathways for differential expression on any gene expression data set and tools to visualize the results.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
14 14 exported
Complexity
10.6 avg / 27 max
Call network
14 nodes / 6 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
61,698
Files
56
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
14
Internal functions
0
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.10.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
32
First release
2010-10-18
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 18
- Examples that run
- 100%18 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 17%
Also includes 2 demo scripts (run with demo())
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| annLoi2008 | matrix | 227 × 5 | No other package |
| classLoi2008 | vector | 255 elements | No other package |
| exprLoi2008 | matrix | 227 × 255 | No other package |
| grListKEGG | list | 2 elements | No other package |
Topics
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("DEGraph")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1214/11-aoas528.
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.