plaid
Bioc currentPLAID ultrafast gene set enrichment scoring
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
PLAID (Pathway Level Average Intensity Detection) is an ultra-fast method to compute single-sample enrichment scores for gene expression or proteomics data. For each sample, plaid computes the gene set score as the average intensity of the genes/proteins in the gene set. The output is a gene set score matrix suitable for further analyses.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
27 15 exported
Complexity
6.9 avg / 30 max
Call network
27 nodes / 43 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
5,457
Files
63
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
15
Internal functions
12
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
1.27
testthat edition
3
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
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
4.3.3
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-04-28
Latest release
2026-04-28
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 93%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Antonino Zito maintainer
- Ivo Kwee author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("plaid")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.