SPIA
Bioc currentSignaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
Release Lineage
Entered 2.4 · Apr 21, 2009
Current · Requires R 4.6
Description
This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
5 4 exported
Complexity
15.8 avg / 32 max
Call network
5 nodes / 3 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
1,299
Files
28
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
4
Internal functions
1
Testing & CI
Has tests
No
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
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.14.0
System requirements
–
C++ standard
–
License
file LICENSE
License flags
SPDX valid, not OSI
History
Versions
35
First release
2009-04-20
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
- 100%
- Documented parameters
- 100%
- Return-value docs
- 75%
- References docs
- 43%
Topics
Depended on by (3)
Bioconductor (3)
People
Adi Laurentiu Tarca