APL
Bioc currentAssociation Plots
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
APL is a package developed for computation of Association Plots (AP), a method for visualization and analysis of single cell transcriptomics data. The main focus of APL is the identification of genes characteristic for individual clusters of cells from input data. The package performs correspondence analysis (CA) and allows to identify cluster-specific genes using Association Plots. Additionally, APL computes the cluster-specificity scores for all genes which allows to rank the genes by their specificity for a selected cell cluster of interest.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
30 14 exported
Complexity
8.7 avg / 34 max
Call network
30 nodes / 38 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
8,783
Files
73
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
21
Internal functions
16
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.10
testthat edition
3
Docs
Roxygen coverage
95.2%
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
4.4.0
System requirements
–
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-10-15
Latest release
2026-04-28
Avg cadence
178 days
Cold removal rate
–
Dep drift
5
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 37 (1 internal)
- Examples that run
- 100%22 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 27%
Repository practices
5 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/vingronlab/apl on 2026-10-11.
GitHub Pages site last deployed 2024-11-04 · The repository has a site deploy workflow
pkgdown site last built 2024-11-04
Topics
People
- Clemens Kohl maintainer author
- Elzbieta Gralinska author
- Martin Vingron author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("APL")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.