SEMPLR
SNP Effect Matrix Pipeline in R
Bioconductor version: 3.23 · Package version: 1.0.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SEMPLR")Details
| Maintainer | Grace Kenney <kenney.grace6@gmail.com> |
| Author | Grace Kenney [aut, cre] (ORCID: <https://orcid.org/0009-0009-6308-3150>), Douglas Phanstiel [aut], NIH NIGMS [fnd], NSF GRFP [fnd] |
| License | MIT + file LICENSE |
| URL | https://github.com/grkenney/SEMPLR, https://grkenney.github.io/SEMPLR |
| Bug Reports | https://www.github.com/grkenney/SEMPLR/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GenomicVariation, MotifAnnotation, SNP, Software, Transcription |
| Package Short Url | https://bioconductor.org/packages/SEMPLR/ |
Citation
From within R, enter citation("SEMPLR"):
Grace Kenney, Douglas Phanstiel. SEMPLR: SNP Effect Matrix Pipeline in R. doi:10.18129/B9.bioc.SEMPLR, R package version 1.0.1, https://bioconductor.org/packages/SEMPLR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | SEMPLR_1.0.1.tar.gz |
| Windows binary (x86_64) | SEMPLR_1.0.1.zip |
| macOS binary (arm64) | SEMPLR_1.0.1.tgz |
| macOS binary (x86_64) | SEMPLR_1.0.1.tgz |
Dependencies
Depends: R (>= 4.1.0)
Imports: BiocGenerics, Biostrings, GenomeInfoDb, AnnotationDbi, ggplot2, ggrepel, VariantAnnotation, GenomicRanges, GenomicFeatures, data.table, methods, scales, S4Vectors, stats, rlang, stringi, universalmotif, Rcpp, ggtree
LinkingTo: Rcpp
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