SEMPLR
This is the development version of SEMPLR; to use it, please install the devel version of Bioconductor.
SNP Effect Matrix Pipeline in R
Bioconductor version: Development (3.23)
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.
Author: Grace Kenney [aut, cre]
, Douglas Phanstiel [aut], NIH NIGMS [fnd], NSF GRFP [fnd]
Maintainer: Grace Kenney <kenney.grace6 at gmail.com>
citation("SEMPLR")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("SEMPLR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SEMPLR")| SEMPLR Vignette | HTML | R Script |
| Reference Manual |
Details
| biocViews | GenomicVariation, MotifAnnotation, SNP, Software, Transcription |
| Version | 0.99.2 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | MIT + file LICENSE |
| 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 |
| System Requirements | |
| URL | https://github.com/grkenney/SEMPLR https://grkenney.github.io/SEMPLR |
| Bug Reports | https://www.github.com/grkenney/SEMPLR/issues |
See More
| 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 |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SEMPLR_0.99.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/SEMPLR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SEMPLR |
| Bioc Package Browser | https://code.bioconductor.org/browse/SEMPLR/ |
| Package Short Url | https://bioconductor.org/packages/SEMPLR/ |
| Package Downloads Report | Download Stats |