atSNP

DOI: 10.18129/B9.bioc.atSNP    

This is the development version of atSNP; to use it, please install the devel version of Bioconductor.

Affinity test for identifying regulatory SNPs

Bioconductor version: Development (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 (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.1
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License GPL-2
Depends R (>= 3.6)
Imports Rcpp, data.table, BiocParallel, BiocFileCache, rappdirs, BSgenome, motifStack, grDevices, graphics, stats, utils, grid
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_1.1.1.tar.gz
Windows Binary atSNP_1.1.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) atSNP_1.1.1.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 http://bioconductor.org/packages/atSNP/
Package Downloads Report Download Stats

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