Package: SEMPLR 1.1.1

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_1.1.1.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_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SEMPLR/json (API)
NEWS

# 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-1.1.0(bioc 3.24)SEMPLR-1.0.0(bioc 3.23)

motifannotationtranscriptionsnpgenomicvariationcpp

4.93 score 1 stars 2 scripts 185 downloads 22 exports 131 dependencies

Last updated from:0bc12fab38. Checks:1 NOTE, 13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE383
linux-devel-arm64OK561
linux-devel-x86_64OK669
source / vignettesOK495
linux-release-arm64OK561
linux-release-x86_64OK682
macos-release-arm64OK477
macos-release-x86_64OK982
macos-oldrel-arm64OK483
macos-oldrel-x86_64OK749
windows-develOK566
windows-releaseOK548
windows-oldrelOK657
wasm-releaseOK343

Exports:convertSEMsToPPMsenrichmentSetsenrichSEMsgetBaselinegetRangesgetRangeSeqsgetSEMgetSEMIdgetSEMsloadSEMCollectionplotEnrichplotSEMplotSEMMotifsplotSEMVariantsscoreBindingscoresscoreVariantssemDataSEMScoresshowSNPEffectMatrixSNPEffectMatrixCollection

Dependencies:abindAnnotationDbiapeaplotaskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibcachemcigarilloclicodetoolscpp11crayoncurldata.tableDBIDelayedArraydigestdplyrevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverformatRfsfutile.loggerfutile.optionsgdtoolsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggfunggiraphggplot2ggplotifyggrepelggtreegluegridGraphicsgtablehighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimenlmeopensslpatchworkpillarpkgconfigpngpurrrR6rappdirsRColorBrewerRcppRcppThreadRCurlrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsyssystemfontstibbletidyrtidyselecttidytreetinytextreeioUCSC.utilsuniversalmotifutf8VariantAnnotationvctrsviridisLitewithrxfunXMLXVectoryamlyulab.utils

SEMPLR Vignette

Rendered fromSEMPLR.Rmdusingknitr::rmarkdownon May 11 2026.

Last update: 2026-02-24
Started: 2026-02-02

Readme and manuals

Help Manual

Help pageTopics
Convert a SNP Effect Matrix to a position probability matrices (PPMs)convertSEMsToPPMs
Run the Full Differential‐Expression Motif Enrichment PipelineenrichmentSets
Calculates binding enrichment for motif(s)enrichSEMs
Access baseline from a SNPEffectMatrix objectgetBaseline getBaseline,SNPEffectMatrix-method
Access ranges slot in a SEMScores objectgetRanges getRanges,SEMScores-method
Get sequence for genomic ranges and variantsgetRangeSeqs
Access the SEM from a SNPEffectMatrix objectgetSEM getSEM,SNPEffectMatrix-method
Access semId from a SNPEffectMatrix objectgetSEMId getSEMId,SNPEffectMatrix-method
Access sems matrix from a SNPEffectMatrixCollection objectgetSEMs getSEMs,SNPEffectMatrixCollection-method
Load .sem files and meta data into a SNPEffectMatrixCollectionloadSEMCollection
Plot the results of 'enrichSEMs'plotEnrich
Plot SEM scores for each nucleic acid in each position of the motifplotSEM
Plot non-alt versus alt binding propensity for a single variantplotSEMMotifs
Plot non-alt versus alt binding propensity for a single motifplotSEMVariants
Calculate binding propensity for all SEM motifs and genomic positions providedscoreBinding
Calculate risk/non-risk binding propensity for all SEM motifs and variants providedscoreVariants
Default SNP Effect Matrix Data CollectionSEMC
Accessor semData slot in a SEMScores objectsemData semData,SEMScores-method semData,SNPEffectMatrixCollection-method
SEMScores object and constructorSEMScores
Class for storing SEM motif binding calculations for multiple genomic ranges or variantsSEMScores-class
Show method for SEMScores objectsshow,SEMScores-method
Show for SNPEffectMatrixshow,SNPEffectMatrix-method
Show method for SNPEffectMatrixCollection objectsshow,SNPEffectMatrixCollection-method
SNPEffectMatrix object and constructorSNPEffectMatrix
SNP Effect Matrix (SEM)SNPEffectMatrix-class
SNPEffectMatrixCollection object and constructorSNPEffectMatrixCollection
A collection of SNPEffectMatrix objects and their corresponding meta dataSNPEffectMatrixCollection-class