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atSNP

Affinity test for identifying regulatory SNPs


Bioconductor version: Release (3.19)

atSNP performs affinity tests of motif matches with the SNP or the reference genomes and SNP-led changes in motif matches.

Author: Chandler Zuo [aut], Sunyoung Shin [aut, cre], Sunduz Keles [aut]

Maintainer: Sunyoung Shin <sunyoung.shin at utdallas.edu>

Citation (from within R, enter citation("atSNP")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("atSNP")

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("atSNP")
atsnp-vignette.html HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, GenomeAnnotation, MotifAnnotation, Software, Visualization
Version 1.20.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL-2
Depends R (>= 3.6)
Imports BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testthat, utils, lifecycle
System Requirements
URL https://github.com/sunyoungshin/atSNP
Bug Reports https://github.com/sunyoungshin/atSNP/issues
See More
Suggests BiocStyle, knitr, rmarkdown
Linking To Rcpp
Enhances
Depends On Me
Imports Me
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Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package atSNP_1.20.0.tar.gz
Windows Binary atSNP_1.20.0.zip (64-bit only)
macOS Binary (x86_64) atSNP_1.20.0.tgz
macOS Binary (arm64) atSNP_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/atSNP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/atSNP
Bioc Package Browser https://code.bioconductor.org/browse/atSNP/
Package Short Url https://bioconductor.org/packages/atSNP/
Package Downloads Report Download Stats