atSNP
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see atSNP.
Affinity test for identifying regulatory SNPs
Bioconductor version: 3.9
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 | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, GenomeAnnotation, MotifAnnotation, Software, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| License | GPL-2 |
| Depends | R (>= 3.6) |
| Imports | Rcpp, data.table, BiocParallel, BiocFileCache, rappdirs, BSgenome, motifStack, grDevices, graphics, stats, utils, grid |
| 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_1.0.0.tar.gz |
| Windows Binary | atSNP_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | atSNP_1.0.0.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 3.9 | Source Archive |