SEMPLR
Bioc currentSNP Effect Matrix Pipeline in R
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
SEMPLR computes transcription factor binding affinity scores for genomic positions and genetic variants. Scores are computed from SNP Effect Matrices (SEMs) produced by SEMpl. 223 pre-computed SEMs are included with the package or custom sets can be provided. Enrichment can be tested among sets of genomic positions to determine if transcription factor binding events occur more often than expected. Comparing binding affinity scores between alleles can reveal differences in transcription factor binding with genetic variation. This package also includes several visualization functions to view scores both on the motif and variant/position level.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
71 14 exported
Complexity
2.7 avg / 8 max
Call network
71 nodes / 64 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
7,872
Files
321
Compiled share
2.1%
Has compiled src
Yes
Language breakdown
API
Exported functions
21
Internal functions
52
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.60
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
–
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-05-16
Latest release
2026-05-16
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
- 100%
- Documented parameters
- 99%
- Return-value docs
- 95%
- References docs
- 0%
Topics
People
- Grace Kenney author maintainer
- NIH NIGMS fnd
- NSF GRFP fnd
- Douglas Phanstiel author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("SEMPLR")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.