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>

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

Installation

To install this package, start R (version "3.6") 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 1.2.0
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, testit, utils
System Requirements
URL https://github.com/sunyoungshin/atSNP
Bug Reports https://github.com/sunyoungshin/atSNP/issues
See More
Suggests testthat, BiocStyle, knitr, rmarkdown
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 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
Bioc Package Browser https://code.bioconductor.org/browse/atSNP/
Package Short Url https://bioconductor.org/packages/atSNP/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive