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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
27 15 exported
Complexity
6 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
5,485
Files
51
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
15
Internal functions
12
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
1.25
testthat edition
3
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
2026-08-11
Latest release
2026-08-11
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
- Help pages
- 25
- Examples that run
- 93%14 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
4 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/bigomics/plaid on 2026-10-21.
GitHub Pages site last deployed 2025-12-10 · The repository has a site deploy workflow
Datasets
Topics
People
- Antonino Zito maintainer
- Ivo Kwee author
Cite
Cite this package
Run in R for the authors' entry:
citation("plaid")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btaf621.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.