clipper
Bioc currentGene Set Analysis Exploiting Pathway Topology
Release Lineage
Entered 2.12 · Apr 4, 2013
Current · Requires R 4.6
Description
Implements topological gene set analysis using a two-step empirical approach. It exploits graph decomposition theory to create a junction tree and reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it "clips" the whole pathway identifying the signal paths having the greatest association with a specific phenotype.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
48 15 exported
Complexity
3.7 avg / 13 max
Call network
48 nodes / 58 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
2,587
Files
57
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
15
Internal functions
33
Testing & CI
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
10%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.15.0
System requirements
–
C++ standard
–
License
AGPL-3
License flags
SPDX valid, OSI approved
History
Versions
27
First release
2013-04-03
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 93%
- Documented parameters
- 99%
- Return-value docs
- 93%
- References docs
- 73%
Depended on by (1)
Bioconductor (1)
People
Paolo Martini
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("clipper")Cite the R Observatory
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