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.
None published for Bioconductor
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
7,870
Files
311
Compiled share
2.1%
Has compiled src
Yes
Language breakdown
API
Exported functions
21
Internal functions
52
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.60
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
–
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
- Help pages
- 29 (2 internal)includes a package overview page
- Examples that run
- 100%23 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 99%
- Return-value docs
- 95%
- Help pages citing references
- 0%
- SEMPLR Vignette HTML
- Adjusted
enrichSEMs()function to only consider the highest scoring binding
orientation for each sequence/SEM combination in enrichment calculations
- Documentation updates to
scoreVariants(),enrichSEMs(), and the vignette. - Fixed bug in
plotSEMMotifs()that was mislabeling plotted motifs with
scores for both reverse and forward orientations
From NEWS.md in the release
Repository practices
7 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/grkenney/semplr on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows
GitHub Pages site last deployed 2026-05-17 · The repository has a site deploy workflow
pkgdown site last built 2026-05-17
Datasets
Topics
People
- Grace Kenney author maintainer
- NIH NIGMS funder
- NSF GRFP funder
- Douglas Phanstiel author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("SEMPLR")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 v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.