atSNP

DOI: 10.18129/B9.bioc.atSNP    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see atSNP.

Affinity test for identifying regulatory SNPs

Bioconductor version: 3.10

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML	R Script	atsnp-vignette.html
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, GenomeAnnotation, MotifAnnotation, Software, Visualization
Version	1.2.0
In Bioconductor since	BioC 3.9 (R-3.6) (1 year)
License	GPL-2
Depends	R (>= 3.6)
Imports	BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testit, utils
LinkingTo	Rcpp
Suggests	testthat, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/sunyoungshin/atSNP
BugReports	https://github.com/sunyoungshin/atSNP/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	atSNP_1.2.0.tar.gz
Windows Binary	atSNP_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	atSNP_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/atSNP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/atSNP
Package Short Url	https://bioconductor.org/packages/atSNP/
Package Downloads Report	Download Stats