JohnsonKinaseData
Bioc currentKinase PWMs based on data published by Johnson et al. 2023 and Yaron-Barir et al. 2024
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
The packages provides position specific weight matrices (PWMs) for 303 human serine/threonine and 93 tyrosine kinases originally published in Johnson et al. 2023 (doi:10.1038/s41586-022-05575-3) and Yaron-Barir et al. 2024 (doi:10.1038/s41586-024-07407-y). The package includes basic functionality to score user provided phosphosites. It also includes pre-computed PWM scores ("background scores") for a large collection of curated human phosphosites which can be used to rank PWM scores relative to the background scores ("percentile rank").
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
10 6 exported
Complexity
2.1 avg / 5 max
Call network
10 nodes / 4 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
1,012
Files
24
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
6
Internal functions
4
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.05
testthat edition
3
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
–
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
5
First release
2024-04-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 7 (1 internal)includes a package overview page
- Examples that run
- 100%6 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 29%
- JohnsonKinaseData HTML
Repository practices
Checks run against github.com/fgeier/johnsonkinasedata on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| metadata | data.frame | 8 × 17 | No other package |
Topics
People
- Florian Geier author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("JohnsonKinaseData")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.
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