source("http://bioconductor.org/biocLite.R")
biocLite("FunciSNP")

FunciSNP

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

Bioconductor version: 2.13

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:

source("http://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		UCSC_genomeviewer_glioma.pdf
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, DataImport, DataRepresentation, Infrastructure, SequenceMatching, Software
Version	1.4.0
In Bioconductor since	BioC 2.11 (R-2.15)
License	GPL-3
Depends	R (>= 2.14.0), ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene, FunciSNP.data
Imports	AnnotationDbi, IRanges, Rsamtools(>= 1.6.1), rtracklayer(>= 1.14.1), methods, ChIPpeakAnno(>= 2.2.0), GenomicRanges, VariantAnnotation, plyr, org.Hs.eg.db, snpStats, ggplot2 (>= 0.9.0), reshape (>= 0.8.4), scales
Suggests
System Requirements
URL	http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source	FunciSNP_1.4.0.tar.gz
Windows Binary	FunciSNP_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	FunciSNP_1.4.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats