Package: SEMPLR
Title: SNP Effect Matrix Pipeline in R
Version: 1.1.2
Authors@R: c(
    person("Grace", "Kenney", 
    email = "kenney.grace6@gmail.com", 
    role = c("aut", "cre"),
    comment = c(ORCID = "0009-0009-6308-3150")),
    person("Douglas", "Phanstiel", 
    role = c("aut")),
    person("NIH NIGMS", role = "fnd"),
    person("NSF GRFP", role = "fnd"))
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.
Imports: BiocGenerics, Biostrings, GenomeInfoDb, AnnotationDbi,
        ggplot2, ggrepel, VariantAnnotation, GenomicRanges,
        GenomicFeatures, data.table, methods, scales, S4Vectors, stats,
        rlang, stringi, universalmotif, Rcpp, ggtree
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat (>= 3.0.0),
        IRanges, BSgenome.Hsapiens.UCSC.hg38,
        BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg38.knownGene,
        org.Hs.eg.db
VignetteBuilder: knitr
License: MIT + file LICENSE
Config/testthat/edition: 3
URL: https://github.com/grkenney/SEMPLR,
        https://grkenney.github.io/SEMPLR
BugReports: https://www.github.com/grkenney/SEMPLR/issues
biocViews: MotifAnnotation, Transcription, SNP, GenomicVariation
LazyData: true
LinkingTo: Rcpp
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-05-17 00:12:20 UTC
RemoteUrl: https://github.com/bioc/SEMPLR
RemoteRef: HEAD
RemoteSha: fcecf410ed0390191b132ba9d8370eb4c9c3e7c5
NeedsCompilation: yes
Packaged: 2026-06-10 06:29:02 UTC; root
Author: Grace Kenney [aut, cre] (ORCID:
    <https://orcid.org/0009-0009-6308-3150>),
  Douglas Phanstiel [aut],
  NIH NIGMS [fnd],
  NSF GRFP [fnd]
Maintainer: Grace Kenney <kenney.grace6@gmail.com>
Depends: R (>= 4.1.0)