FunciSNP

DOI: 10.18129/B9.bioc.FunciSNP    

Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs

Bioconductor version: Release (3.6)

FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in coding or non-coding regions.

Author: Simon G. Coetzee <simon at simoncoetzee.com> and Houtan Noushmehr, PhD <houtan at usp.br>

Maintainer: Simon G. Coetzee <simon at simoncoetzee.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("FunciSNP")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("FunciSNP")

 

PDF	R Script	FunciSNP Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, DataImport, DataRepresentation, Infrastructure, SequenceMatching, Software
Version	1.22.0
In Bioconductor since	BioC 2.11 (R-2.15) (5.5 years)
License	GPL-3
Depends	R (>= 2.14.0), ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene, FunciSNP.data
Imports	methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools(>= 1.6.1), rtracklayer(>= 1.14.1), ChIPpeakAnno(>= 2.2.0), VariantAnnotation, plyr, snpStats, ggplot2 (>= 0.9.0), reshape (>= 0.8.4), scales
LinkingTo
Suggests	org.Hs.eg.db
SystemRequirements
Enhances	parallel
URL	http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	FunciSNP_1.22.0.tar.gz
Windows Binary	FunciSNP_1.22.0.zip
Mac OS X 10.11 (El Capitan)	FunciSNP_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/FunciSNP
Package Short Url	http://bioconductor.org/packages/FunciSNP/
Package Downloads Report	Download Stats