atSNP
Bioc currentAffinity test for identifying regulatory SNPs
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
atSNP performs affinity tests of motif matches with the SNP or the reference genomes and SNP-led changes in motif matches.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
60 9 exported
Complexity
7.4 avg / 25 max
Call network
60 nodes / 83 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
6,205
Files
47
Compiled share
26.5%
Has compiled src
Yes
Language breakdown
API
Exported functions
9
Internal functions
9
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.42
testthat edition
–
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
3.6
System requirements
–
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-05-02
Latest release
2026-04-28
Avg cadence
182 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
- 21includes a package overview page
- Examples that run
- 89%8 run in a plain check · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 5%
- atsnp-vignette.html HTML
Repository practices
Checks run against github.com/sunyoungshin/atsnp on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| encode_motif | list | 2,065 elements | No other package |
| encode_motifinfo | vector | 2,065 elements | No other package |
| jaspar_motif | list | 593 elements | No other package |
| jaspar_motifinfo | vector | 593 elements | No other package |
| motif_library | list | 2 elements | No other package |
| motif_match | data.frame | 1 × 35 | No other package |
| motif_scores | list | 2 elements | No other package |
| prior | vector | 4 elements | No other package |
| snpInfo | list | 10 elements | No other package |
| snp_tbl | data.frame | 2 × 5 | No other package |
| transition | matrix | 4 × 4 | No other package |
Topics
People
- Sunyoung Shin author maintainer
- Sunduz Keles author
- Chandler Zuo author
Cite
Cite this package
Run in R for the authors' entry:
citation("atSNP")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btv328.
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.