Package: SEMPLR 1.1.2

Grace Kenney

SEMPLR: SNP Effect Matrix Pipeline in R

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.

Authors:Grace Kenney [aut, cre], Douglas Phanstiel [aut], NIH NIGMS [fnd], NSF GRFP [fnd]

SEMPLR_1.1.2.tar.gz
SEMPLR_1.1.2.zip(r-4.7)SEMPLR_1.1.2.zip(r-4.6)SEMPLR_1.1.2.zip(r-4.5)
SEMPLR_1.1.2.tgz(r-4.6-x86_64)SEMPLR_1.1.2.tgz(r-4.6-arm64)SEMPLR_1.1.2.tgz(r-4.5-x86_64)SEMPLR_1.1.2.tgz(r-4.5-arm64)
SEMPLR_1.1.2.tar.gz(r-4.7-arm64)SEMPLR_1.1.2.tar.gz(r-4.7-x86_64)SEMPLR_1.1.2.tar.gz(r-4.6-arm64)SEMPLR_1.1.2.tar.gz(r-4.6-x86_64)
SEMPLR_1.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SEMPLR/json (API)

# Install 'SEMPLR' in R:

install.packages('SEMPLR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/grkenney/semplr/issues

Pkgdown/docs site:https://grkenney.github.io

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

SEMC - Default SNP Effect Matrix Data Collection

On BioConductor:SEMPLR-1.1.2(bioc 3.24)SEMPLR-1.0.1(bioc 3.23)

motifannotation transcription snp genomicvariation cpp

4.93 score 1 stars 2 scripts 168 downloads 22 exports 131 dependencies

Last updated from:fcecf410ed. Checks:12 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	382
linux-devel-arm64	NOTE	559
linux-devel-x86_64	NOTE	634
source / vignettes	OK	536
linux-release-arm64	NOTE	566
linux-release-x86_64	NOTE	670
macos-release-arm64	NOTE	492
macos-release-x86_64	NOTE	820
macos-oldrel-arm64	NOTE	428
macos-oldrel-x86_64	NOTE	947
windows-devel	NOTE	500
windows-release	NOTE	507
windows-oldrel	NOTE	550
wasm-release	OK	371

Exports:convertSEMsToPPMs enrichmentSets enrichSEMs getBaseline getRanges getRangeSeqs getSEM getSEMId getSEMs loadSEMCollection plotEnrich plotSEM plotSEMMotifs plotSEMVariants scoreBinding scores scoreVariants semData SEMScores show SNPEffectMatrix SNPEffectMatrixCollection

Dependencies:abind AnnotationDbi ape aplot askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome bslib cachem cigarillo cli codetools cpp11 crayon curl data.table DBI DelayedArray digest dplyr evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver formatR fs futile.logger futile.options gdtools generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggfun ggiraph ggplot2 ggplotify ggrepel ggtree glue gridGraphics gtable highr htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nlme openssl patchwork pillar pkgconfig png purrr R6 rappdirs RColorBrewer Rcpp RcppThread RCurl restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys systemfonts tibble tidyr tidyselect tidytree tinytex treeio UCSC.utils universalmotif utf8 VariantAnnotation vctrs viridisLite withr xfun XML XVector yaml yulab.utils

SEMPLR Vignette

Rendered fromSEMPLR.Rmdusingknitr::rmarkdown

Last update: 2026-05-16
Started: 2026-02-02

Help page	Topics
Convert a SNP Effect Matrix to a position probability matrices (PPMs)	convertSEMsToPPMs
Run the Full Differential‐Expression Motif Enrichment Pipeline	enrichmentSets
Calculates binding enrichment for motif(s)	enrichSEMs
Access baseline from a SNPEffectMatrix object	getBaseline getBaseline,SNPEffectMatrix-method
Access ranges slot in a SEMScores object	getRanges getRanges,SEMScores-method
Get sequence for genomic ranges and variants	getRangeSeqs
Access the SEM from a SNPEffectMatrix object	getSEM getSEM,SNPEffectMatrix-method
Access semId from a SNPEffectMatrix object	getSEMId getSEMId,SNPEffectMatrix-method
Access sems matrix from a SNPEffectMatrixCollection object	getSEMs getSEMs,SNPEffectMatrixCollection-method
Load .sem files and meta data into a SNPEffectMatrixCollection	loadSEMCollection
Plot the results of 'enrichSEMs'	plotEnrich
Plot SEM scores for each nucleic acid in each position of the motif	plotSEM
Plot non-alt versus alt binding propensity for a single variant	plotSEMMotifs
Plot non-alt versus alt binding propensity for a single motif	plotSEMVariants
Calculate binding propensity for all SEM motifs and genomic positions provided	scoreBinding
Calculate risk/non-risk binding propensity for all SEM motifs and variants provided	scoreVariants
Default SNP Effect Matrix Data Collection	SEMC
Accessor semData slot in a SEMScores object	semData semData,SEMScores-method semData,SNPEffectMatrixCollection-method
SEMScores object and constructor	SEMScores
Class for storing SEM motif binding calculations for multiple genomic ranges or variants	SEMScores-class
Show method for SEMScores objects	show,SEMScores-method
Show for SNPEffectMatrix	show,SNPEffectMatrix-method
Show method for SNPEffectMatrixCollection objects	show,SNPEffectMatrixCollection-method
SNPEffectMatrix object and constructor	SNPEffectMatrix
SNP Effect Matrix (SEM)	SNPEffectMatrix-class
SNPEffectMatrixCollection object and constructor	SNPEffectMatrixCollection
A collection of SNPEffectMatrix objects and their corresponding meta data	SNPEffectMatrixCollection-class

Package: SEMPLR 1.1.2

SEMPLR: SNP Effect Matrix Pipeline in R

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)